Contacts of the strand formed by residues 37 - 48 (chain A) in PDB entry 2VBJ
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 HIS 37 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A ILE* 3.8 28.0 - - + -
28A GLU 3.1 9.2 - - - +
29A PRO* 3.7 22.5 - - + +
30A ASN 3.9 2.1 + - - +
33A TYR* 3.5 17.1 - - - +
35A PHE* 2.8 29.1 + - - +
36A LYS* 1.3 92.4 + - + +
38A ARG* 1.3 60.2 + - - +
122A PHE* 3.9 22.4 - - + -
143A THR* 4.1 7.5 - - + +
147A THR* 4.6 8.9 + - - +
148A VAL* 3.9 37.9 + - + +
150A ALA* 5.3 7.9 - - + -
151A VAL 5.8 0.9 - - - -
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Residues in contact with ARG 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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27A ILE* 3.5 2.9 - - - -
28A GLU* 2.8 72.3 + - + +
33A TYR* 3.5 47.6 + - + -
37A HIS* 1.3 73.3 - - - +
39A LEU* 1.3 77.6 + - - +
40A LYS* 3.3 28.5 + - - +
122A PHE* 4.9 2.5 - - - -
20C C 4.0 0.8 - - - +
21C C 4.4 1.0 - - - +
3E A 3.3 19.9 + - - +
4E G 2.5 52.7 + - - -
5E G 3.5 0.2 + - - -
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Residues in contact with LEU 39 (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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26A GLN 3.4 4.3 - - - +
27A ILE* 3.8 28.0 - - + -
38A ARG* 1.3 89.2 + - - +
40A LYS* 1.3 60.2 + - - +
41A LEU* 4.3 12.3 - - + +
108A ILE* 4.5 3.6 - - + -
112A LEU* 3.8 24.2 - - + -
115A ALA* 5.4 1.3 - - + -
122A PHE* 4.0 22.4 - - + -
125A VAL* 3.5 31.9 - - + -
126A CYS* 4.0 15.0 - - - -
129A VAL* 4.2 9.6 - - + -
3E A 5.7 1.2 + - - -
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Residues in contact with LYS 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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24A ILE 3.8 1.0 - - - +
25A ALA* 3.5 1.4 - - - -
26A GLN* 2.8 59.8 + - + +
28A GLU* 3.3 11.0 + - + +
38A ARG* 3.3 25.5 - - - +
39A LEU* 1.3 75.1 - - - +
41A LEU* 1.3 64.7 + - - +
42A THR* 4.7 7.6 + - - +
79A SER* 6.0 2.9 - - - -
19C T 2.8 31.3 + - + +
20C C 3.0 10.1 - - - +
4E G 4.7 1.6 - - + +
5E G 2.3 40.4 + - - -
6E A 3.4 6.7 - - - +
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Residues in contact with LEU 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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24A ILE 3.4 3.4 - - - +
25A ALA* 3.9 22.4 - - + -
26A GLN 4.7 0.4 - - - +
39A LEU* 4.3 8.0 - - + -
40A LYS* 1.3 89.2 - - - +
42A THR* 1.3 61.7 + - - +
79A SER* 3.0 28.3 - - - +
81A ILE* 3.9 24.9 - - + +
84A LEU* 3.8 16.5 - - + +
105A VAL* 4.1 17.7 - - + -
108A ILE* 3.9 34.1 - - + -
109A THR* 4.0 13.7 - - - +
112A LEU* 4.5 7.6 - - + -
129A VAL* 5.1 2.2 - - + -
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Residues in contact with THR 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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22A SER 3.7 0.5 - - - +
23A ILE* 3.7 3.5 - - - +
24A ILE* 2.8 50.6 + - + +
26A GLN* 4.6 10.3 + - - -
40A LYS* 4.7 6.8 - - - +
41A LEU* 1.3 79.1 + - - +
43A PHE* 1.3 74.1 + - - +
44A LYS* 4.2 7.6 - - + -
77A ILE* 3.9 32.1 - - + -
78A LEU 3.7 3.6 - - - +
79A SER* 4.2 5.7 - - - -
84A LEU* 5.1 2.2 - - - -
105A VAL* 6.2 0.2 - - - +
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Residues in contact with PHE 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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13A LEU* 5.2 1.1 - - + -
17A VAL* 3.5 43.1 - - + -
22A SER 3.6 2.9 - - - -
23A ILE* 4.1 20.6 - - + +
42A THR* 1.3 73.4 - - - +
44A LYS* 1.3 63.4 + - - +
45A VAL* 3.7 15.0 - - + -
58A LEU* 5.5 0.2 - - + -
62A ILE* 4.3 3.1 - - + -
76A TYR* 3.6 31.6 - + - -
77A ILE* 3.5 4.0 - - - -
78A LEU* 2.9 38.5 + - + +
84A LEU* 3.7 23.6 - - + +
87A PHE* 3.4 38.1 - + - -
88A LEU* 4.5 7.0 - - + -
91A LEU* 4.4 3.8 - - + -
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Residues in contact with LYS 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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21A GLY* 3.2 2.8 - - - -
22A SER* 2.8 45.5 + - - +
24A ILE* 4.1 11.4 - - + +
42A THR* 4.2 7.4 - - + -
43A PHE* 1.3 78.2 - - - +
45A VAL* 1.3 63.7 + - - +
46A THR* 3.8 8.3 - - - +
70A GLU* 5.2 2.6 + - - -
75A ASN* 3.1 36.9 + - - +
76A TYR 3.3 7.4 - - - +
77A ILE* 3.9 20.2 - - + -
15C A 4.8 1.9 + - + -
16C G 2.9 44.7 + - + +
17C G 3.7 19.2 + - - -
8E C 5.3 0.4 - - - +
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Residues in contact with VAL 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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13A LEU* 5.3 0.4 - - + -
16A PHE* 3.7 32.8 - - + -
17A VAL* 4.2 12.6 - - + -
20A ASP 4.1 8.5 - - - +
21A GLY* 4.4 2.5 - - - -
43A PHE* 3.7 27.8 - - + -
44A LYS* 1.3 78.6 - - - +
46A THR* 1.3 65.5 + - - +
55A LEU* 3.7 21.1 - - + +
58A LEU* 4.1 17.7 - - + -
75A ASN* 3.3 4.3 - - - -
76A TYR* 2.9 35.7 + - + -
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Residues in contact with THR 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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20A ASP* 3.3 14.8 + - - +
22A SER* 6.0 0.2 - - - -
44A LYS* 3.8 4.3 - - - +
45A VAL* 1.3 76.3 - - - +
47A GLN* 1.3 80.1 + - - +
73A VAL* 4.0 16.2 - - + -
74A SER 3.4 8.1 - - - +
75A ASN* 2.6 24.7 + - - +
14C A 3.2 49.2 - - + +
15C A 3.6 20.7 - - - +
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Residues in contact with GLN 47 (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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16A PHE* 3.5 16.1 - - + -
20A ASP* 2.9 23.0 + - - +
46A THR* 1.3 86.7 + - - +
48A LYS* 1.3 63.3 + - - +
51A ARG* 2.8 45.4 + - + +
54A PHE* 5.3 3.1 - - + -
55A LEU* 4.0 23.5 - - + +
73A VAL* 4.2 3.6 - - - -
74A SER* 2.7 43.6 + - - +
18B ASP 4.8 1.9 - - - +
97B LEU* 3.4 15.9 - - + +
14C A 3.2 21.7 + - - +
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Residues in contact with LYS 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 GLN* 1.3 73.0 - - - +
49A THR* 1.3 57.2 + - - +
50A GLN* 3.1 31.1 + - + +
51A ARG* 2.7 38.9 + - - +
52A ARG 3.6 1.9 + - - -
72A SER* 3.7 13.9 - - - +
73A VAL* 4.1 5.6 - - - +
137B ASP* 3.5 31.3 + - - +
13C G 3.2 45.6 + - + +
14C A 2.8 22.0 + - - +
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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