Contacts of the strand formed by residues 38 - 49 (chain A) in PDB entry 2V8W
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 PRO 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A ILE* 5.4 3.6 - - + -
36A LYS 3.4 9.3 - - - +
37A HIS* 1.3 86.9 - - + +
39A LEU* 1.3 64.7 + - - +
67A ASP 3.7 6.7 - - - +
68A THR* 4.3 6.3 - - + -
52B ILE* 3.4 22.3 - - + +
54B TYR* 2.6 33.5 + - - +
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Residues in contact with LEU 39 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A PRO* 1.3 76.4 - - - +
40A GLN* 1.3 66.6 + - - +
41A ASN* 3.3 18.0 + - - +
43A TRP* 3.8 25.1 - - + +
66A PHE* 3.9 20.9 - - + -
67A ASP* 2.8 28.5 + - - +
68A THR 3.8 7.6 - - - +
69A VAL* 3.8 30.5 - - + +
138A ILE* 3.7 34.5 - - + +
52B ILE* 4.0 7.7 - - - +
54B TYR* 3.9 10.1 - - + -
59B LEU* 4.9 0.2 - - + -
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Residues in contact with GLN 40 (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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39A LEU* 1.3 72.7 - - - +
41A ASN* 1.3 66.5 + - - +
138A ILE 4.8 2.8 + - - -
140A GLU* 3.3 42.0 - - + +
147A ASP* 5.2 3.5 + - - +
51B ARG* 3.4 27.7 + - + +
52B ILE* 2.8 52.7 + - - +
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Residues in contact with ASN 41 (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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39A LEU* 3.3 19.2 - - - +
40A GLN* 1.3 89.6 + - - +
42A ARG* 1.3 63.5 + - - +
43A TRP* 3.2 36.2 - - + +
67A ASP* 4.0 4.1 - - - -
95A LYS* 3.6 30.3 + - + +
140A GLU* 2.8 27.2 + - - +
147A ASP* 5.4 1.6 - - - +
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Residues in contact with ARG 42 (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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41A ASN* 1.3 78.4 + - - +
43A TRP* 1.3 68.0 + - - +
65A LYS* 3.8 38.0 + - + +
66A PHE* 3.4 15.6 - - - +
67A ASP* 3.8 32.1 + - + +
95A LYS* 3.6 5.7 - - - +
96A ASP* 2.9 47.1 + - + +
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Residues in contact with TRP 43 (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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39A LEU* 3.8 16.9 - - + +
41A ASN* 3.2 37.5 + - + +
42A ARG* 1.3 75.9 - - - +
44A ALA* 1.3 60.0 + - - +
45A LEU 4.3 0.2 - - - -
65A LYS* 3.2 6.6 - - - +
66A PHE* 2.9 51.3 + - + -
93A LEU* 3.8 17.9 - - + -
94A PHE 3.5 7.9 - - - -
95A LYS* 3.4 49.8 - - + -
96A ASP 4.5 1.3 - - - -
137A LEU* 3.3 53.6 - - + -
138A ILE* 3.8 20.9 + - + +
140A GLU* 3.7 12.9 + - - -
149A VAL* 4.6 5.8 - - + -
150A CYS 4.1 5.2 - - - -
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Residues in contact with ALA 44 (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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43A TRP* 1.3 75.4 - - - +
45A LEU* 1.3 59.9 - - - +
46A TRP* 3.4 25.4 - - + +
62A LEU* 3.7 16.8 - - + -
64A SER 3.4 4.9 - - - -
65A LYS* 4.0 15.7 - - + +
93A LEU* 3.4 5.0 - - - +
94A PHE 2.8 33.2 + - - +
95A LYS 5.4 0.4 - - - +
96A ASP* 4.4 8.3 - - - +
98A ILE 6.0 0.2 - - - +
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Residues in contact with LEU 45 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A TRP 4.3 0.2 - - - -
44A ALA* 1.3 72.2 - - - +
46A TRP* 1.3 57.0 + - - +
62A LEU* 3.6 3.3 - - - +
63A ILE* 2.7 53.2 + - + +
64A SER 2.8 18.4 + - - +
66A PHE* 4.9 0.6 - - + -
75A LEU* 4.0 25.6 - - + -
79A ILE* 3.2 34.1 - - + -
91A TYR* 4.3 18.4 - - + -
92A SER 3.4 18.8 - - - +
93A LEU* 3.9 18.3 - - + +
130A TRP* 4.7 6.7 - - + +
134A LEU* 5.2 4.0 - - + -
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Residues in contact with TRP 46 (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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44A ALA* 3.4 31.3 + - + +
45A LEU* 1.3 75.7 - - - +
47A PHE* 1.3 61.6 + - - +
60A LEU* 4.1 28.9 - - + -
61A ARG 3.4 8.7 - - - -
62A LEU* 3.5 46.9 - - + -
63A ILE* 4.3 2.5 - - - -
65A LYS* 6.0 2.0 - - - -
91A TYR* 3.4 10.7 - - - -
92A SER* 2.8 39.6 + - - +
94A PHE* 4.4 4.0 - - - +
98A ILE 4.4 8.3 + - - -
99A GLU* 4.2 28.0 - - + -
100A PRO* 3.5 39.2 - - + +
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Residues in contact with PHE 47 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A TRP* 1.3 74.5 - - - +
48A PHE* 1.3 61.7 + - - +
49A LYS* 3.6 27.4 - - + -
59A ASN 3.5 2.0 - - - +
60A LEU* 3.6 4.2 - - - -
61A ARG* 2.7 42.8 + - + +
63A ILE* 3.8 20.6 - - + +
85A LEU* 4.0 21.3 - - + -
89A CYS* 3.5 37.9 - - + -
90A ASP 3.3 12.3 - - - -
91A TYR* 4.0 16.4 - + - -
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Residues in contact with PHE 48 (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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47A PHE* 1.3 77.8 - - - +
49A LYS* 1.3 59.6 + - - +
50A ASN* 3.6 27.8 - - + -
56A TRP* 3.1 63.9 - + - -
59A ASN* 3.4 31.4 - - + -
60A LEU* 4.1 15.5 - - + -
88A GLY 3.6 15.0 - - - -
89A CYS* 3.0 27.5 - - - +
90A ASP* 3.0 40.0 + - + +
157A ARG* 5.1 5.4 - - - -
1218A MGO 6.0 0.2 - - - -
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Residues in contact with LYS 49 (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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47A PHE* 3.6 20.4 - - + -
48A PHE* 1.3 75.4 - - - +
50A ASN* 1.3 77.6 + - - +
51A ASP* 4.4 1.6 - - - +
59A ASN* 3.3 28.0 + - - +
86A MET* 3.2 39.3 - - - +
89A CYS* 3.7 18.8 - - - -
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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