Contacts of the helix formed by residues 316 - 331 (chain A) in PDB entry 4WGK
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 SER 316 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A THR* 3.6 16.5 - - - +
136A ARG 4.2 3.2 + - - -
137A LEU* 3.9 8.7 - - - -
140A ARG* 5.7 0.5 + - - -
159A ASP* 3.8 27.4 + - - -
193A THR* 5.1 0.3 + - - -
195A THR* 3.5 14.8 - - - -
315A ASN* 1.3 73.9 - - - +
317A ASP* 1.3 70.4 + - - +
319A VAL* 3.9 6.6 - - - +
320A GLY* 3.1 36.2 + - - -
715A TRP* 3.8 1.0 + - - -
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Residues in contact with ASP 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A THR* 4.0 4.9 - - - +
196A HIS 5.0 0.5 + - - -
197A SER* 4.6 2.9 + - - -
304A PRO* 3.1 32.9 - - + +
305A VAL* 3.6 1.0 - - - -
306A SER* 3.0 21.4 + - - -
307A MET* 3.0 33.6 + - - +
315A ASN* 2.7 17.3 + - - +
316A SER* 1.3 82.2 - - - +
318A ASN* 1.3 81.1 + - - +
321A TYR 2.9 24.3 + - - -
397A THR* 3.5 11.7 - - - -
715A TRP* 3.3 9.0 - - - -
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Residues in contact with ASN 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A ILE* 4.3 3.7 - - - +
303A HIS 3.3 20.8 + - - -
304A PRO* 3.4 11.5 - - - +
306A SER* 3.2 18.3 + - - +
317A ASP* 1.3 95.2 + - - +
319A VAL* 1.3 85.4 + - - +
321A TYR* 3.2 1.8 + - - -
322A ALA* 3.0 23.4 + - - +
355A PRO* 3.6 10.1 - - - +
397A THR* 3.5 24.5 - - - +
400A ILE* 4.0 8.4 - - + +
401A GLY* 3.4 10.8 - - - +
404A MET* 3.7 17.0 - - + -
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Residues in contact with VAL 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A THR* 4.1 25.1 - - + +
300A PHE* 5.5 2.5 - - + +
302A ILE* 3.7 24.7 - - + +
304A PRO* 4.0 19.5 - - + -
316A SER 3.9 9.4 - - - +
318A ASN* 1.3 95.9 + - - +
320A GLY* 1.3 61.4 + - - +
322A ALA* 3.5 4.1 + - - +
323A SER* 3.0 31.1 + - - -
345A PHE* 3.8 23.4 - - + +
346A ALA 6.4 0.9 - - - -
347A SER* 6.6 0.7 - - - -
404A MET* 3.8 13.5 - - + -
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Residues in contact with GLY 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ARG* 4.9 2.6 + - - -
159A ASP* 4.7 6.5 - - - -
316A SER* 3.1 43.8 + - - -
319A VAL* 1.3 78.4 - - - +
321A TYR* 1.3 58.3 + - - +
323A SER* 3.4 7.5 + - - -
324A TYR* 2.9 27.2 + - - +
715A TRP* 4.1 1.5 + - - -
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Residues in contact with TYR 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A ASP 2.9 12.1 + - - +
318A ASN* 3.2 10.1 + - - +
320A GLY* 1.3 73.7 - - - +
322A ALA* 1.3 61.5 + - - +
324A TYR* 3.2 24.2 - + - +
325A LEU* 2.9 58.7 + - + +
397A THR 4.6 2.0 - - - +
398A GLN* 3.5 65.3 + - + +
401A GLY* 4.0 1.8 - - - -
402A ARG* 4.0 19.3 + - + -
715A TRP* 3.5 40.1 - + + -
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Residues in contact with ALA 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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318A ASN 3.0 13.5 + - - +
319A VAL* 3.6 5.8 - - - +
320A GLY 3.2 0.2 - - - -
321A TYR* 1.3 74.1 - - - +
323A SER* 1.3 64.3 + - - +
325A LEU* 3.3 2.6 + - - +
326A LEU* 3.0 28.2 + - - +
345A PHE* 3.5 31.4 - - + -
401A GLY 3.3 25.5 + - - +
404A MET* 4.3 2.7 - - + -
405A TYR* 3.9 8.7 - - - +
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Residues in contact with SER 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ARG* 3.7 20.1 + - - -
319A VAL 3.0 15.5 + - - -
320A GLY* 3.5 8.4 - - - -
322A ALA* 1.3 76.2 - - - +
324A TYR* 1.3 62.2 + - - +
326A LEU* 3.5 4.5 + - - +
327A GLU* 3.0 32.7 + - - +
343A ALA 3.2 17.9 - - - -
344A ALA* 4.1 0.5 - - - -
345A PHE* 3.3 29.9 + - - +
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Residues in contact with TYR 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A THR* 5.0 1.3 - - - -
138A TYR* 6.4 2.2 - + - -
140A ARG* 5.5 0.2 - - - +
320A GLY 2.9 14.8 + - - +
321A TYR* 3.2 27.4 - + - +
323A SER* 1.3 78.1 - - - +
325A LEU* 1.3 68.2 + - + +
327A GLU* 3.6 6.2 + - - +
328A GLN* 3.0 51.3 + - + +
336A PRO* 3.7 33.6 - - + +
337A GLY 5.9 0.7 - - - -
713A ALA* 3.8 7.4 - - + -
714A SER* 3.8 5.9 - - - -
715A TRP* 3.4 51.2 + + + +
716A GLU* 3.9 15.1 + - - +
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Residues in contact with LEU 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A TYR* 2.9 59.1 + - + +
322A ALA 3.8 1.1 - - - +
324A TYR* 1.3 86.2 - - + +
326A LEU* 1.3 65.7 + - - +
328A GLN* 3.9 4.2 - - + +
329A GLU* 3.0 26.7 + - - +
402A ARG* 3.8 31.2 - - + +
405A TYR* 3.5 43.2 - - + -
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Residues in contact with LEU 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A LEU* 3.9 34.8 - - + -
322A ALA 3.0 14.9 + - - +
323A SER 3.8 1.1 - - - +
325A LEU* 1.3 77.6 - - - +
327A GLU* 1.3 60.7 + - - +
329A GLU* 3.4 4.5 + - - +
330A LYS* 3.2 33.0 + - - +
341A PHE* 4.8 1.6 - - + -
343A ALA* 3.7 18.6 - - + -
345A PHE* 3.4 33.2 - - + -
405A TYR* 3.5 33.4 - - + +
408A ALA* 4.0 6.1 - - + -
409A LYS* 4.1 18.8 - - + +
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Residues in contact with GLU 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ARG* 2.9 34.2 + - - -
138A TYR* 5.4 2.1 - - - -
140A ARG* 2.9 32.6 + - - -
323A SER 3.0 20.8 + - - +
324A TYR* 4.0 5.6 - - - +
326A LEU* 1.3 75.9 - - - +
328A GLN* 1.3 60.8 + - - +
330A LYS 3.4 0.3 + - - -
331A ASN* 2.8 47.4 + - - +
337A GLY* 5.1 5.7 + - - -
338A GLN 5.7 0.9 - - - +
341A PHE* 3.9 10.3 - - - +
342A VAL* 3.7 1.4 - - - -
343A ALA* 3.2 31.1 + - + +
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Residues in contact with GLN 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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324A TYR* 3.0 46.6 + - + +
325A LEU* 4.0 5.6 - - + +
326A LEU 3.4 0.2 - - - -
327A GLU* 1.3 81.0 - - + +
329A GLU* 1.3 62.7 + - - +
331A ASN* 3.9 15.2 - - - +
332A LYS* 4.0 5.5 + - - +
334A TYR 3.6 20.8 + - - +
335A LEU 3.6 2.6 - - - +
336A PRO* 3.4 41.6 - - - +
337A GLY 4.6 1.0 + - - -
338A GLN 4.6 4.5 - - - +
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Residues in contact with GLU 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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325A LEU 3.0 18.1 + - - +
326A LEU* 3.8 6.8 - - - +
328A GLN* 1.3 77.9 - - - +
330A LYS* 1.3 73.4 + - - +
332A LYS* 3.4 21.4 - - - +
405A TYR* 3.2 22.3 + - - +
409A LYS* 3.2 48.6 + - - +
178B LYS* 5.6 4.2 - - - -
236B THR* 5.8 1.4 - - - +
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Residues in contact with LYS 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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293A ASP* 3.5 28.3 - - + +
296A LEU* 5.3 2.2 - - - +
326A LEU* 3.2 17.4 + - + +
327A GLU 4.0 0.4 - - - +
329A GLU* 1.3 94.6 + - + +
331A ASN* 1.3 59.7 + - - +
332A LYS* 3.0 10.7 + - - +
341A PHE* 3.7 42.2 - - + -
409A LYS* 5.4 6.5 - - - +
412A TYR* 3.7 29.4 - - - +
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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
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108A ARG* 4.5 0.8 - - - +
327A GLU* 2.8 31.1 + - - +
328A GLN* 3.9 10.2 - - - +
330A LYS* 1.3 68.5 - - - +
332A LYS* 1.3 66.7 + - - +
334A TYR* 3.0 36.7 + - + +
338A GLN 3.6 7.6 + - - +
339A GLY* 3.5 21.9 + - - -
340A PRO* 3.2 11.3 - - - +
341A PHE* 3.0 51.2 + - - +
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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
------------------------------------------------------------
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