Contacts of the helix formed by residues 317 - 334 (chain A) in PDB entry 1NVP
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 VAL 317 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258A MET* 3.3 9.2 - - - -
315A ALA* 3.5 14.9 - - - +
316A LYS* 1.3 91.4 - - + +
318A ARG* 1.3 63.5 + - - +
319A ALA* 3.3 11.2 + - + +
320A GLU* 3.3 37.6 + - + +
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Residues in contact with ARG 318 (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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165A LEU* 3.5 29.9 - - + +
225A LYS 4.9 0.8 + - - -
226A SER* 4.4 12.3 - - - -
227A GLU* 2.8 45.8 + - - +
258A MET* 3.4 13.7 - - + +
317A VAL* 1.3 74.0 - - - +
319A ALA* 1.3 62.9 + - - +
321A ILE* 3.0 17.8 + - - +
322A TYR* 2.9 55.1 + - + -
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Residues in contact with ALA 319 (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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317A VAL* 3.3 12.1 - - + +
318A ARG* 1.3 77.7 - - - +
320A GLU* 1.3 54.4 + - + +
322A TYR* 3.2 11.7 + - - +
323A GLU* 2.7 42.8 + - - +
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Residues in contact with GLU 320 (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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298A PRO* 3.3 26.2 - - + +
299A ARG 5.3 1.9 - - - +
300A ILE* 3.9 16.9 - - + +
314A GLY 4.6 0.7 - - - +
315A ALA* 3.3 4.9 - - + -
316A LYS* 2.8 35.9 + - - +
317A VAL* 3.6 26.1 - - + +
318A ARG 3.2 0.6 - - - -
319A ALA* 1.3 77.0 - - + +
321A ILE* 1.3 57.5 + - - +
323A GLU* 4.3 5.4 - - - +
324A ALA* 2.9 32.9 + - - +
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Residues in contact with ILE 321 (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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163A PRO* 3.8 24.9 - - + -
165A LEU* 4.2 21.5 - - + -
258A MET* 3.7 17.3 - - + +
260A GLY* 4.3 13.9 - - - +
300A ILE* 4.5 5.2 - - + -
312A LEU* 3.6 36.8 - - + +
315A ALA* 3.4 28.9 - - + -
317A VAL 4.4 1.6 - - - +
318A ARG* 3.0 12.7 + - - +
320A GLU* 1.3 78.6 - - - +
322A TYR* 1.3 66.1 + - + +
324A ALA* 4.7 2.2 - - - -
325A PHE* 3.2 19.1 + - - +
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Residues in contact with TYR 322 (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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162A VAL* 3.9 17.1 - - + +
163A PRO* 3.5 46.8 + - + -
165A LEU* 5.4 2.6 - - + +
318A ARG* 2.9 61.8 + - + -
319A ALA* 3.2 10.2 + - - +
321A ILE* 1.3 79.9 - - + +
323A GLU* 1.3 66.1 + - - +
325A PHE* 3.2 4.0 + - - +
326A GLU* 3.0 31.7 + - + +
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Residues in contact with GLU 323 (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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297A LYS* 4.1 24.1 + - - +
298A PRO* 3.6 29.9 - - + +
319A ALA* 2.7 25.0 + - + +
320A GLU* 3.9 6.7 - - - +
322A TYR* 1.3 74.6 - - - +
324A ALA* 1.3 61.5 + - - +
326A GLU* 3.2 7.0 + - - +
327A ASN* 3.0 36.3 + - - +
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Residues in contact with ALA 324 (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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295A MET* 3.3 32.7 - - + +
298A PRO* 3.9 3.6 - - + +
300A ILE* 3.7 30.7 - - + -
302A LEU* 4.3 0.8 - - + +
312A LEU* 3.9 6.7 - - + -
320A GLU 2.9 20.2 + - - +
321A ILE 3.9 3.6 - - - +
323A GLU* 1.3 76.6 - - - +
325A PHE* 1.3 57.4 + - - +
327A ASN 3.3 0.2 + - - -
328A ILE* 3.0 24.3 + - - +
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Residues in contact with PHE 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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159A SER* 3.6 23.1 - - - -
161A ILE* 3.9 25.4 - - + -
163A PRO* 3.7 32.3 - - + -
262A CYS* 3.3 28.9 - - - -
264A VAL* 4.0 18.4 - - + -
310A VAL* 4.6 8.7 - - + -
312A LEU* 3.7 12.3 - - + +
321A ILE 3.2 11.5 + - - +
322A TYR 3.7 2.0 - - - +
324A ALA* 1.3 75.1 - - - +
326A GLU* 1.3 68.3 + - - +
328A ILE* 3.9 16.2 - - + -
329A TYR* 3.0 47.2 + + + +
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Residues in contact with GLU 326 (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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159A SER* 3.9 27.2 + - - +
161A ILE 4.6 4.5 - - - +
163A PRO* 5.9 0.9 - - - +
322A TYR* 3.0 23.5 + - + +
323A GLU* 3.7 7.9 - - - +
325A PHE* 1.3 83.9 - - - +
327A ASN* 1.3 65.0 + - - +
329A TYR* 4.1 3.3 - - - +
330A PRO* 3.1 20.4 - - - +
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Residues in contact with ASN 327 (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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295A MET* 3.6 17.0 - - + +
297A LYS* 2.8 29.7 + - - +
298A PRO* 3.9 3.2 - - - +
323A GLU* 3.0 23.7 + - - +
324A ALA 3.5 8.3 - - - +
326A GLU* 1.3 80.6 - - - +
328A ILE* 1.3 60.3 + - - +
330A PRO* 3.5 15.4 - - - +
331A ILE* 3.8 11.3 - - - +
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Residues in contact with ILE 328 (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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273A LEU* 6.1 0.4 - - + -
293A TYR* 4.6 17.3 - - + -
295A MET* 4.0 8.3 - - + +
302A LEU* 3.1 35.0 - - + -
304A ILE* 3.7 29.6 - - + -
310A VAL* 5.2 1.6 - - + -
324A ALA 3.0 12.5 + - - +
325A PHE* 3.5 23.1 - - + +
327A ASN* 1.3 76.8 - - - +
329A TYR* 1.3 68.0 + - - +
330A PRO 3.4 0.2 - - - -
331A ILE* 3.2 12.4 + - + +
332A LEU* 2.9 49.4 + - + +
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Residues in contact with TYR 329 (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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159A SER* 4.3 33.7 - - - +
161A ILE* 4.9 5.1 - - + +
264A VAL* 3.9 32.5 + - + -
266A PHE* 4.2 12.0 - + - -
325A PHE* 3.0 41.7 + + + +
326A GLU* 4.1 4.0 - - - +
328A ILE* 1.3 79.0 - - - +
330A PRO* 1.3 66.5 - - + +
332A LEU* 3.1 5.8 + - + +
333A LYS* 2.9 70.8 + - + +
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Residues in contact with PRO 330 (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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326A GLU 3.1 19.1 - - - +
327A ASN* 3.5 10.8 - - - +
329A TYR* 1.3 96.1 - - + +
331A ILE* 1.3 66.8 + - + +
333A LYS* 3.3 19.3 + - - +
334A GLY* 3.2 17.5 + - - -
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Residues in contact with ILE 331 (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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273A LEU* 3.6 21.5 - - + -
277A HIS* 3.6 35.7 - - + +
293A TYR* 5.0 12.6 - - + +
327A ASN 3.8 16.2 - - - +
328A ILE* 3.2 13.6 + - + +
330A PRO* 1.3 79.8 - - + +
332A LEU* 1.3 61.5 + - + +
334A GLY* 3.2 6.1 + - - -
335A PHE* 3.1 27.8 - - + -
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Residues in contact with LEU 332 (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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264A VAL* 4.0 24.0 - - + -
266A PHE* 3.6 19.8 - - + -
268A ILE* 4.3 13.9 - - + +
273A LEU* 3.9 27.8 - - + -
304A ILE* 3.9 16.6 - - + -
310A VAL* 4.1 15.7 - - + -
328A ILE* 2.9 51.2 + - + +
329A TYR* 3.1 5.8 + - - +
331A ILE* 1.3 74.9 - - + +
333A LYS* 1.3 65.4 + - - +
334A GLY 3.0 1.6 - - - -
335A PHE* 2.9 16.5 + - - +
336A ARG 3.4 7.6 + - - -
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Residues in contact with LYS 333 (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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266A PHE* 3.7 17.0 - - + -
269A ARG* 5.2 0.2 + - - -
329A TYR* 2.9 59.1 + - + +
330A PRO* 3.7 18.2 - - - +
331A ILE 3.3 0.2 - - - -
332A LEU* 1.3 76.3 - - - +
334A GLY* 1.3 58.3 + - - +
335A PHE 3.0 5.4 + - - -
336A ARG* 3.2 16.5 + - - +
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Residues in contact with GLY 334 (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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269A ARG* 3.6 13.8 + - - -
330A PRO 3.2 9.1 + - - -
331A ILE 3.2 8.8 + - - -
332A LEU 3.0 1.6 - - - -
333A LYS* 1.3 78.0 - - - +
335A PHE* 1.3 70.8 + - - +
336A ARG 3.7 0.4 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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