Contacts of the strand formed by residues 44 - 53 (chain B) in PDB entry 1PVS
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 TYR 44 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40B ALA* 3.2 3.6 - - - -
41B VAL* 2.7 47.7 + - + +
42B GLY 3.3 0.2 - - - -
43B GLU* 1.3 86.4 - - + +
45B ARG* 1.3 59.0 + - - +
66B GLY 3.5 19.1 - - - +
67B LEU* 3.5 4.5 - - + +
69B PRO* 3.5 31.4 - - + +
70B VAL* 3.7 38.8 - - + -
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Residues in contact with ARG 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LEU 3.3 5.4 - - - +
40B ALA* 3.5 18.8 - - + +
42B GLY 3.6 17.6 + - - -
43B GLU* 3.0 41.6 + - - +
44B TYR* 1.3 78.8 - - - +
46B GLY* 1.3 58.8 + - - +
66B GLY* 3.4 25.5 + - - -
67B LEU* 3.5 6.5 - - - +
144B GLU* 2.9 34.8 + - - -
145B ARG 5.9 0.4 - - - -
146B LEU* 3.7 16.2 - - + -
148B ASP* 5.4 3.1 - - - +
154B CYS* 3.8 17.4 - - - +
157B THR* 4.9 12.5 - - - +
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Residues in contact with GLY 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B SER* 3.3 5.9 - - - -
39B LEU 2.9 29.9 + - - -
45B ARG* 1.3 77.4 - - - +
47B VAL* 1.3 64.6 + - - -
64B SER* 3.3 13.0 - - - -
67B LEU* 3.7 9.1 - - - +
146B LEU* 3.6 16.1 - - - +
148B ASP* 5.5 2.7 - - - -
149B PHE* 5.3 2.0 - - - -
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Residues in contact with VAL 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B ALA* 4.4 2.9 - - + -
37B ARG 3.6 14.6 - - - +
38B SER* 4.7 0.2 - - - -
46B GLY* 1.3 77.7 - - - +
48B VAL* 1.3 74.0 + - - +
49B THR* 4.1 10.6 + - - +
62B ASN* 3.7 1.4 + - - +
63B LEU* 3.6 4.3 - - - -
64B SER* 3.2 33.7 + - - -
67B LEU* 3.8 1.1 - - - +
146B LEU* 3.7 13.7 - - + -
149B PHE* 3.9 17.3 - - + -
152B TYR* 3.5 42.0 - - + +
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Residues in contact with VAL 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B TYR* 3.8 1.9 - - - +
36B ALA* 3.0 23.4 - - - -
37B ARG* 3.0 15.1 + - + +
39B LEU* 3.4 32.3 - - + -
47B VAL* 1.3 72.3 - - - +
49B THR* 1.3 63.8 + - - +
50B ALA 4.2 0.4 + - - -
61B ILE* 4.0 6.5 - - + -
62B ASN 3.5 2.5 - - - -
63B LEU* 3.5 22.9 - - + -
67B LEU* 3.5 20.9 - - + -
74B CYS* 4.5 1.8 - - + -
78B MET* 3.6 41.6 - - + +
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Residues in contact with THR 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A THR* 5.5 1.8 - - - +
251A ALA* 4.1 20.2 - - + +
252A GLN* 5.8 0.2 - - + -
34B TYR* 4.2 17.0 - - + -
35B TYR 3.3 8.1 - - - +
36B ALA* 3.7 9.8 - - + +
47B VAL* 4.3 7.8 + - - +
48B VAL* 1.3 76.6 - - - +
50B ALA* 1.3 61.4 + - - +
51B ILE* 3.9 21.4 - - + +
60B HIS 3.6 0.7 - - - +
61B ILE* 3.2 7.3 - - - +
62B ASN* 2.8 54.2 + - - +
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Residues in contact with ALA 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B TRP* 5.9 0.7 - - + -
34B TYR* 3.3 6.4 - - - +
35B TYR* 2.6 40.8 + - + +
48B VAL 4.2 0.2 - - - -
49B THR* 1.3 73.4 - - - +
51B ILE* 1.3 61.3 + - - +
52B PRO* 3.8 4.0 - - - +
59B LEU* 4.1 10.5 - - + -
60B HIS 3.5 3.8 - - - -
61B ILE* 4.4 6.5 - - + -
78B MET* 4.3 12.6 - - - -
82B PHE* 3.8 32.3 - - + -
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Residues in contact with ILE 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A ALA* 3.9 25.6 - - + +
252A GLN* 4.1 22.9 - - + +
255A ARG* 4.2 21.5 - - + -
1B MET* 4.8 8.1 - - - -
33B SER* 4.1 10.8 - - - +
34B TYR* 4.1 8.5 - - + -
49B THR* 3.9 18.4 - - + +
50B ALA* 1.3 77.0 - - - +
52B PRO* 1.3 69.6 - - - +
53B ASP* 3.8 0.7 + - + -
59B LEU* 3.5 3.9 - - - +
60B HIS* 2.7 48.4 + - + +
62B ASN* 5.4 0.4 - - + -
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Residues in contact with PRO 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B TRP* 3.8 6.7 - - + -
12B TRP* 3.6 54.5 - - + +
16B LEU* 5.1 4.9 - - + -
33B SER* 3.3 25.0 - - - +
34B TYR* 4.5 0.9 - - - -
50B ALA 3.8 4.9 - - - +
51B ILE* 1.3 95.0 - - - +
53B ASP* 1.3 58.7 + - - +
54B ILE* 3.6 10.3 + - + +
58B THR 3.9 2.9 - - - +
59B LEU* 3.7 9.2 - - + -
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Residues in contact with ASP 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A ARG* 3.4 23.4 + - - +
282A ALA* 5.0 6.6 - - - +
6B TRP* 3.9 2.0 - - - -
51B ILE* 6.3 0.2 - - + -
52B PRO* 1.3 71.1 - - - +
54B ILE* 1.3 61.7 + - - +
55B ALA* 3.7 6.1 + - - +
56B ARG* 3.0 39.5 + - - +
57B HIS* 2.9 17.0 + - - -
58B THR* 2.9 27.6 + - - +
60B HIS* 4.1 9.9 - - - +
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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