Contacts of the strand formed by residues 357 - 369 (chain A) in PDB entry 2H4Q
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 GLY 357 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197A ALA 3.3 11.7 - - - -
198A GLU 4.1 0.2 - - - -
199A TRP* 3.4 23.4 + - - -
249A TYR* 4.5 0.2 - - - -
353A VAL* 3.8 0.2 - - - -
354A ASP* 3.1 34.4 + - - +
356A LYS* 1.3 79.7 - - - +
358A THR* 1.3 67.9 + - - -
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Residues in contact with THR 358 (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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195A PHE* 4.1 4.6 - - + +
196A LYS* 3.4 5.8 - - - +
197A ALA 3.0 30.7 + - - +
199A TRP* 3.6 9.7 - - - -
249A TYR* 2.7 35.2 + - - +
256A MET* 4.2 0.7 - - + -
351A VAL* 3.8 16.6 - - + -
352A ALA 3.3 11.2 - - - +
353A VAL* 3.8 11.3 - - + +
354A ASP* 6.0 0.2 - - - -
357A GLY* 1.3 79.2 + - - -
359A GLU* 1.3 72.2 + - - +
360A ALA 4.5 0.2 - - - +
391B ILE* 3.9 15.0 - - + -
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Residues in contact with GLU 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A GLU* 4.7 3.1 - - - +
171A LYS* 3.6 32.9 + - + +
194A TYR* 2.6 41.2 + - + +
195A PHE 3.4 7.0 - - - +
196A LYS* 4.1 22.1 + - + +
350A PHE* 3.8 16.6 - - + -
351A VAL* 3.2 4.9 - - - +
352A ALA* 2.8 44.1 + - + +
358A THR* 1.3 72.8 - - - +
360A ALA* 1.3 64.7 + - - +
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Residues in contact with ALA 360 (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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195A PHE* 2.7 45.5 + - + +
350A PHE 3.3 9.0 - - - +
351A VAL* 4.2 7.2 - - + -
358A THR 4.2 0.2 - - - -
359A GLU* 1.3 75.2 - - - +
361A VAL* 1.3 61.1 + - - +
391B ILE* 3.8 18.8 - - + -
401B PHE* 3.5 36.7 - - + -
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Residues in contact with VAL 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A THR* 3.3 36.3 - - + -
171A LYS* 3.6 30.7 - - + -
172A ILE* 4.4 5.3 - - + +
193A ILE 2.9 21.1 - - - +
194A TYR* 3.6 15.3 - - + -
349A SER* 3.5 0.7 - - - -
350A PHE* 2.7 55.3 + - + +
359A GLU* 5.6 0.2 - - + -
360A ALA* 1.3 76.4 - - - +
362A ALA* 1.3 61.6 + - - +
401B PHE* 3.7 6.9 - - - -
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Residues in contact with ALA 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A SER* 3.6 31.2 - - - -
34A SER* 4.2 2.2 - - - -
168A THR* 4.1 4.7 - - - +
172A ILE* 4.8 3.1 - - - -
192A ALA* 3.5 1.9 - - - +
193A ILE* 3.0 34.3 + - + +
347A HIS* 3.7 8.5 - - - +
348A GLN 3.1 14.6 - - - +
349A SER* 4.0 7.4 - - - +
361A VAL* 1.3 79.0 - - - +
363A ALA* 1.3 64.7 + - - +
401B PHE* 4.2 1.3 - - + -
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Residues in contact with ALA 363 (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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34A SER* 3.6 1.6 - - - -
164A VAL* 3.7 30.5 - - + -
168A THR* 4.7 2.0 - - + -
172A ILE* 4.8 2.9 - - + +
175A LEU* 3.8 17.7 - - + +
191A ASN 3.1 13.0 - - - +
192A ALA* 4.4 4.9 - - + -
346A ILE 3.9 0.7 - - - +
347A HIS* 3.2 5.9 - - - -
348A GLN 2.9 31.5 + - - -
362A ALA* 1.3 75.4 - - - +
364A THR* 1.3 64.7 + - - +
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Residues in contact with THR 364 (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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34A SER* 2.7 36.4 + - - -
35A ILE* 3.4 12.3 + - + +
38A ALA* 3.8 16.8 - - + +
175A LEU* 4.6 0.7 - - - -
189A LEU 3.6 1.4 - - - +
190A VAL* 3.2 7.3 - - - +
191A ASN 2.9 32.1 + - - -
345A VAL* 4.0 23.1 - - + -
346A ILE 3.2 10.5 - - - +
347A HIS* 3.0 20.5 - - + -
363A ALA* 1.3 70.8 - - - +
365A ALA* 1.3 63.2 + - - +
366A VAL* 4.1 0.4 - - + -
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Residues in contact with ALA 365 (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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175A LEU* 4.0 13.6 - - + +
176A LEU* 3.6 31.0 - - + -
188A ILE* 4.0 14.8 - - + -
189A LEU 3.5 4.0 - - - -
190A VAL* 4.4 5.2 - - + +
344A LYS 3.7 0.2 - - - +
345A VAL* 3.4 3.0 - - - -
346A ILE* 2.8 38.8 + - + +
363A ALA 4.4 0.2 - - - -
364A THR* 1.3 71.5 - - - +
366A VAL* 1.3 63.0 + - - +
367A ILE* 3.6 4.9 + - + +
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Residues in contact with VAL 366 (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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38A ALA* 3.9 22.7 - - + +
39A LEU* 3.8 24.0 - - + -
42A THR* 3.5 23.3 - - - +
187A LEU 3.7 1.0 - - - +
188A ILE* 3.3 3.5 - - - -
189A LEU* 2.8 36.5 + - + +
342A ILE* 4.2 24.7 - - + -
344A LYS 3.7 3.6 - - - +
345A VAL* 4.4 9.4 - - + +
364A THR* 4.8 0.2 - - + -
365A ALA* 1.3 70.8 - - - +
367A ILE* 1.3 61.4 + - - +
368A ILE* 3.8 20.4 + - + +
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Residues in contact with ILE 367 (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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176A LEU* 3.9 15.9 - - + -
180A ASP* 3.7 45.3 - - + +
185A THR* 3.9 24.9 - - + +
187A LEU 3.7 2.5 - - - -
188A ILE* 4.2 19.1 - - + -
342A ILE* 3.6 3.6 - - - +
343A SER* 2.8 47.0 + - - +
344A LYS* 2.8 34.1 + - + +
346A ILE* 4.1 5.2 - - + -
365A ALA 4.1 6.7 - - - +
366A VAL* 1.3 72.3 - - - +
368A ILE* 1.3 57.5 + - - +
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Residues in contact with ILE 368 (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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42A THR* 4.5 10.1 - - + -
185A THR* 3.9 2.3 - - - +
186A ARG* 2.9 5.5 + - - -
187A LEU* 2.7 54.0 + - + +
189A LEU* 4.1 27.1 - - + -
331A PHE* 5.2 7.6 - - + -
334A MET* 5.0 10.1 - - - -
340A LEU* 3.8 36.3 - - + -
341A ALA 3.4 13.5 - - - +
342A ILE* 4.2 11.2 - - + -
343A SER* 4.6 0.9 - - - -
366A VAL* 4.1 17.0 - - + +
367A ILE* 1.3 79.9 - - - +
369A SER* 1.3 62.0 + - - +
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Residues in contact with SER 369 (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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184A THR* 3.5 39.0 - - - -
185A THR* 4.2 2.2 - - - +
186A ARG* 3.9 15.5 - - - +
339A ASP 3.4 13.2 - - - +
340A LEU* 3.6 9.4 - - - -
341A ALA* 3.0 33.9 + - - +
343A SER* 4.3 16.7 + - - -
367A ILE 4.3 0.6 + - - -
368A ILE* 1.3 75.2 - - - +
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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
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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