Contacts of the helix formed by residues 308 - 331 (chain A) in PDB entry 4ND1
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 308 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A SER* 3.8 17.9 - - - -
306A ASP* 5.5 2.5 - - - +
307A LEU* 1.3 74.8 - - - +
309A PRO* 1.3 66.2 - - + +
310A LEU* 3.7 9.3 + - - +
311A GLU* 2.9 39.6 + - - +
312A GLN* 2.8 33.0 + - - +
403A GOL 5.5 1.0 - - - -
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Residues in contact with PRO 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A LEU 4.5 0.2 - - - +
308A THR* 1.3 85.9 - - + +
310A LEU* 1.3 56.7 + - - +
312A GLN* 3.4 19.0 + - + +
313A LYS* 3.0 28.2 + - - +
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Residues in contact with LEU 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A THR* 3.1 8.4 + - - +
309A PRO* 1.3 78.6 - - - +
311A GLU* 1.3 59.2 + - - +
313A LYS* 3.3 14.4 + - + +
314A LEU* 2.9 48.0 + - + +
403A GOL 4.1 23.3 - - - +
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Residues in contact with GLU 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A VAL* 4.4 13.9 - - + +
202A ALA* 4.2 8.3 - - - -
203A THR* 3.3 4.2 + - - -
204A SER* 2.7 46.0 + - - -
307A LEU* 3.4 19.6 - - + +
308A THR* 2.9 33.0 + - - +
310A LEU* 1.3 74.0 - - - +
312A GLN* 1.3 60.9 + - - +
314A LEU* 3.4 7.8 + - - +
315A LEU* 2.9 29.5 + - - +
403A GOL 2.6 36.5 + - - +
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Residues in contact with GLN 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A LEU* 3.1 38.5 + - + +
308A THR 2.8 21.7 + - - +
309A PRO* 3.6 16.6 - - + +
311A GLU* 1.3 72.3 - - - +
313A LYS* 1.3 57.4 + - - +
315A LEU* 3.6 8.4 + - - +
316A GLY* 3.1 21.7 + - - -
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Residues in contact with LYS 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A PRO 3.0 14.5 + - - +
310A LEU* 3.4 18.8 - - + +
311A GLU 3.2 0.2 - - - -
312A GLN* 1.3 74.8 - - - +
314A LEU* 1.3 65.8 - - + +
316A GLY* 2.9 5.1 + - - -
317A GLU* 2.9 43.2 + - + +
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Residues in contact with LEU 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A GLY 4.2 1.9 - - - +
200A VAL* 3.8 17.3 - - + +
310A LEU* 2.9 42.9 + - + +
311A GLU* 3.8 7.9 - - - +
313A LYS* 1.3 75.1 - - + +
315A LEU* 1.3 62.6 + - - +
317A GLU* 3.3 24.8 + - - +
318A SER* 3.0 21.7 + - - -
403A GOL 3.7 31.6 - - - +
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Residues in contact with LEU 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A ILE* 4.1 13.2 - - + -
193A GLY* 3.8 33.0 - - - +
200A VAL* 3.8 8.6 - - + +
279A TYR* 3.8 44.9 - - + +
287A MET* 4.4 13.9 - - + -
307A LEU* 3.8 14.6 - - + -
311A GLU 2.9 18.1 + - - +
312A GLN* 3.7 7.2 - - - +
314A LEU* 1.3 75.8 - - - +
316A GLY* 1.3 58.3 + - - +
318A SER* 3.1 4.9 + - - -
319A ILE* 2.8 40.4 + - + +
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Residues in contact with GLY 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A GLN 3.1 12.4 + - - -
313A LYS* 2.9 9.6 + - - -
315A LEU* 1.3 75.5 - - - +
317A GLU* 1.3 54.6 + - - +
319A ILE* 3.3 15.3 + - - +
320A ASN* 3.0 35.9 + - - +
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Residues in contact with GLU 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A GLY* 5.7 1.3 - - - -
313A LYS* 2.9 43.2 + - + +
314A LEU* 3.5 26.4 - - - +
315A LEU 3.2 0.2 - - - -
316A GLY* 1.3 73.0 - - - +
318A SER* 1.3 61.0 + - - +
320A ASN* 3.4 14.3 + - - +
321A GLU* 3.0 28.0 + - - +
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Residues in contact with SER 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A GLY* 3.7 7.7 - - - -
194A GLY* 2.9 32.2 + - - -
198A GLY* 3.3 33.7 + - - -
200A VAL* 4.6 0.7 - - - -
314A LEU 3.0 9.0 + - - -
315A LEU* 3.3 11.7 - - - -
317A GLU* 1.3 72.7 - - - +
319A ILE* 1.3 65.9 + - - +
321A GLU* 3.1 10.2 + - - +
322A VAL* 3.0 25.0 + - - +
404A GOL 5.5 0.7 + - - -
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Residues in contact with ILE 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A TYR 4.6 4.9 - - - +
281A VAL* 3.4 30.3 - - + -
285A ILE* 4.4 11.4 - - + -
287A MET* 3.7 24.5 - - + -
315A LEU* 2.8 35.8 + - + +
316A GLY* 3.4 11.9 - - - +
318A SER* 1.3 76.3 - - - +
320A ASN* 1.3 60.3 + - - +
322A VAL* 3.3 8.1 + - - +
323A ASN* 3.0 44.3 + - - +
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Residues in contact with ASN 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A GLY 3.0 25.3 + - - +
317A GLU* 3.5 14.0 - - - +
319A ILE* 1.3 80.2 - - - +
321A GLU* 1.3 53.9 - - - +
323A ASN* 3.8 9.7 + - - +
324A THR* 2.6 40.4 + - - +
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Residues in contact with GLU 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A GLY* 4.1 0.9 - - - -
197A ASP* 3.6 14.7 + - - +
198A GLY* 3.2 35.0 + - - -
317A GLU 3.0 14.4 + - - +
318A SER* 3.1 11.2 + - - +
320A ASN* 1.3 76.3 - - - +
322A VAL* 1.3 59.3 + - - +
324A THR* 3.5 7.8 + - - -
325A ILE* 3.2 33.6 + - + +
404A GOL 3.4 22.0 + - - +
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Residues in contact with VAL 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A ASP* 4.5 10.1 - - + -
144A VAL* 3.8 16.9 - - + +
194A GLY* 4.0 25.8 - - - +
285A ILE* 3.9 22.0 - - + -
286A TYR 4.0 14.4 - - - +
287A MET* 5.1 4.5 - - + -
318A SER 3.0 18.6 + - - +
319A ILE* 3.3 8.7 + - - +
321A GLU* 1.3 75.5 - - - +
323A ASN* 1.3 58.4 + - - +
325A ILE 3.5 1.0 + - - -
326A SER* 2.9 29.4 + - - -
404A GOL 4.0 17.0 - - - +
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Residues in contact with ASN 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A ILE* 3.4 20.6 - - - +
319A ILE* 3.0 39.4 + - - +
320A ASN* 3.8 10.5 + - - +
322A VAL* 1.3 72.9 - - - +
324A THR* 1.3 60.5 + - - +
326A SER* 3.3 8.2 + - - -
327A LYS* 2.8 32.5 + - - +
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Residues in contact with THR 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A ASN* 2.6 24.4 + - - +
321A GLU* 3.6 8.5 - - - -
323A ASN* 1.3 75.4 - - - +
325A ILE* 1.3 69.4 + - + +
327A LYS* 3.2 7.9 + - - +
328A VAL* 3.0 33.3 + - + +
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Residues in contact with ILE 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A ASP* 6.3 0.2 - - - -
110A SER* 3.1 33.7 - - - +
113A LEU* 3.6 26.9 - - + +
141A PRO* 4.4 5.4 - - + -
144A VAL* 3.8 22.6 - - + +
321A GLU* 3.2 21.8 + - + +
322A VAL* 5.0 0.2 - - - -
324A THR* 1.3 84.1 - - + +
326A SER* 1.3 61.2 + - - +
328A VAL* 3.4 12.5 + - + +
329A LEU* 3.2 18.7 + - - +
404A GOL 4.6 9.9 - - - +
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Residues in contact with SER 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A VAL* 3.9 20.1 - - - +
147A SER* 5.6 3.5 + - - -
322A VAL* 2.9 21.9 + - - -
323A ASN* 3.5 11.7 - - - -
324A THR 3.2 0.2 - - - -
325A ILE* 1.3 77.8 - - - +
327A LYS* 1.3 60.4 + - - +
329A LEU* 3.4 4.2 + - - +
330A ASP* 3.2 31.2 + - - +
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Residues in contact with LYS 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A ASN 2.8 18.5 + - - +
324A THR* 3.7 6.3 - - - +
326A SER* 1.3 73.0 - - - +
328A VAL* 1.3 65.3 + - - +
330A ASP* 3.2 15.0 + - + +
331A ASN* 3.2 38.9 + - - +
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Residues in contact with VAL 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A LEU* 3.9 9.9 - - + -
114A PHE* 3.7 25.7 - - + -
324A THR* 3.0 28.5 + - + +
325A ILE* 3.5 15.3 - - + +
327A LYS* 1.3 76.3 - - + +
329A LEU* 1.3 61.8 + - - +
331A ASN* 3.0 28.2 + - - +
332A ALA* 3.2 2.1 + - - -
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Residues in contact with LEU 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A LEU* 3.9 25.8 - - + +
114A PHE* 4.5 3.8 - - + -
117A ALA* 3.6 22.2 - - + -
144A VAL* 3.7 23.6 - - + -
145A MET* 4.2 3.6 - - + -
148A HIS* 3.9 32.5 - - + +
325A ILE 3.2 10.6 + - - +
326A SER 3.6 9.6 - - - +
327A LYS 3.3 0.4 - - - -
328A VAL* 1.3 79.2 - - - +
330A ASP* 1.3 64.2 + - - +
332A ALA* 3.2 30.5 + - + +
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Residues in contact with ASP 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A LYS* 4.5 14.9 + - - -
326A SER* 3.2 22.2 + - - +
327A LYS* 3.2 19.4 + - + +
329A LEU* 1.3 81.5 - - - +
331A ASN* 1.3 65.2 + - - +
332A ALA 3.4 2.0 + - - +
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Residues in contact with ASN 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A PHE* 5.1 1.4 - - - -
327A LYS* 3.2 30.2 + - - +
328A VAL* 3.0 11.8 + - - +
330A ASP* 1.3 82.1 - - - +
332A ALA* 1.3 62.7 + - - +
333A PRO* 4.1 1.6 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il