Contacts of the strand formed by residues 28 - 38 (chain A) in PDB entry 3WJG
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 28 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A LEU 4.2 0.2 - - - -
27A LEU* 1.3 75.0 - - - +
29A THR* 1.3 63.3 - - - -
30A TRP* 3.8 8.2 - - - -
51A ARG* 3.4 4.9 - - - +
52A PHE 3.0 35.4 + - - +
165A LYS* 4.0 9.4 - - - -
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Residues in contact with THR 29 (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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28A GLY* 1.3 76.4 + - - -
30A TRP* 1.3 60.8 + - - +
31A ARG* 5.0 0.4 - - - +
49A GLU* 3.9 25.4 - - + +
50A ILE 3.4 10.3 - - - +
51A ARG* 3.8 22.5 + - + +
165A LYS* 3.7 6.2 - - - +
166A LEU* 2.8 59.5 + - + +
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Residues in contact with TRP 30 (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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25A TYR 3.3 23.1 - - - -
26A LEU* 2.9 25.9 + - + -
28A GLY 3.8 9.2 + - - -
29A THR* 1.3 78.2 - - - +
31A ARG* 1.3 61.0 + - - +
49A GLU* 3.2 8.0 - - - +
50A ILE* 2.8 44.0 + - + +
52A PHE* 3.9 14.2 - + - -
137A LEU* 3.6 22.4 - - + -
140A GLY 3.5 20.2 - - - -
142A LEU* 3.5 37.7 - - + -
163A LEU* 3.6 22.9 - - + -
164A ASP 3.2 5.4 - - - -
165A LYS* 3.5 46.4 - - + +
166A LEU* 4.3 2.2 - - - -
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Residues in contact with ARG 31 (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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29A THR* 5.0 0.8 - - - +
30A TRP* 1.3 74.8 - - - +
32A GLY* 1.3 62.0 + - - +
48A GLU 3.3 11.7 - - - +
49A GLU* 2.9 30.9 + - - +
67A TRP* 3.8 14.9 - - + -
163A LEU* 3.8 4.7 - - - -
164A ASP* 2.9 33.0 + - - +
166A LEU* 3.5 41.6 - - + +
401A GOL 3.4 28.0 - - - +
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Residues in contact with GLY 32 (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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31A ARG* 1.3 76.0 - - - +
33A GLN* 1.3 63.6 + - - +
47A GLY* 3.5 2.4 - - - -
48A GLU* 2.9 29.8 + - - +
162A ILE 3.4 14.1 - - - -
163A LEU* 3.8 5.5 - - - +
164A ASP* 4.7 0.4 - - - -
401A GOL 3.4 24.2 - - - -
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Residues in contact with GLN 33 (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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32A GLY* 1.3 74.1 - - - +
34A GLY* 1.3 61.2 + - - +
45A ARG* 4.9 11.0 + - - +
46A TYR* 3.2 13.2 - - - +
47A GLY* 4.2 0.7 - - - -
48A GLU* 4.4 2.2 - - - +
69A LEU* 3.8 27.2 - - + +
161A ALA* 3.4 5.8 - - - +
162A ILE* 3.1 29.4 + - - +
163A LEU* 4.9 1.0 - - - +
401A GOL 3.0 27.1 + - - +
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Residues in contact with GLY 34 (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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33A GLN* 1.3 77.4 - - - +
35A GLU* 1.3 61.3 + - - +
45A ARG* 3.3 12.2 + - - +
46A TYR* 2.8 47.5 + - - +
160A LYS 3.0 13.7 - - - -
161A ALA* 3.7 3.1 - - - -
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Residues in contact with GLU 35 (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 GLY* 1.3 75.0 - - - +
36A GLY* 1.3 63.7 + - - +
37A GLU* 3.9 10.5 - - + +
43A SER* 3.7 19.9 + - - -
44A PHE 3.2 17.9 - - - +
45A ARG* 2.8 46.1 + - + +
46A TYR* 3.5 6.9 - - - -
158A LEU 3.8 0.3 - - - +
159A LEU* 3.4 2.6 - - - -
160A LYS* 2.9 44.5 + - + +
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Residues in contact with GLY 36 (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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35A GLU* 1.3 75.9 - - - +
37A GLU* 1.3 62.2 + - - +
43A SER* 3.1 7.4 - - - -
44A PHE* 2.8 57.9 + - - +
46A TYR* 4.0 3.0 - - - -
158A LEU 3.1 9.9 - - - -
159A LEU* 3.9 2.7 - - - -
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Residues in contact with GLU 37 (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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35A GLU* 3.9 14.7 - - + +
36A GLY* 1.3 75.4 - - - +
38A TYR* 1.3 69.7 + - - +
41A ILE* 3.8 16.8 - - - +
42A PRO* 5.3 0.2 - - + -
43A SER* 3.9 17.4 + - - +
44A PHE* 4.2 2.0 - - - -
157A PRO 3.3 18.4 - - - +
158A LEU* 2.9 14.2 + - - +
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Residues in contact with TYR 38 (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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37A GLU* 1.3 77.5 - - - +
39A PRO* 1.4 88.0 - - + +
40A THR* 4.2 9.4 - - - -
41A ILE* 2.7 43.2 + - + +
148A TRP* 2.7 50.2 + + + -
149A SER* 3.6 6.6 - - - -
150A THR* 4.2 9.0 - - + -
153A ASN* 3.4 37.9 + - + +
156A GLN* 3.4 22.3 - - + +
157A PRO 3.5 16.2 - - - -
158A LEU* 3.7 21.5 - - + -
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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