Contacts of the strand formed by residues 45 - 53 (chain A) in PDB entry 1MS4
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 VAL 45 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A ASN* 3.4 2.6 - - - +
42A VAL 2.9 34.7 + - - +
44A GLY* 1.3 79.1 - - - +
46A MET* 1.3 73.4 + - - +
47A VAL* 3.6 12.2 + - + +
69A TYR* 4.3 8.3 - - + -
70A SER 3.7 14.1 - - - +
71A VAL* 4.2 4.3 - - + +
138A VAL* 4.1 14.8 - - + -
140A LYS* 3.7 36.6 - - + -
149A ALA* 4.0 22.7 - - + -
151A ILE* 5.7 1.3 - - + -
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Residues in contact with MET 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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39A LEU* 3.9 12.6 - - + -
40A VAL 3.5 4.5 - - - +
44A GLY 3.8 1.8 + - - -
45A VAL* 1.3 74.0 - - - +
47A VAL* 1.3 62.5 + - - +
69A TYR* 3.2 5.6 - - - +
70A SER* 2.7 40.3 + - - +
73A ASP* 3.8 32.8 - - - +
74A GLY 3.8 0.4 - - - -
77A TRP* 3.8 18.6 - - + -
346A LEU* 4.1 17.0 - - + -
348A LYS* 3.9 25.8 - - + -
353A TYR* 4.7 7.9 - - + -
368A PHE* 3.0 39.3 - - + -
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Residues in contact with VAL 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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38A ALA 3.7 2.3 - - - +
39A LEU* 3.7 4.7 - - - +
40A VAL* 2.9 47.5 + - + +
42A VAL* 4.4 10.3 - - + -
45A VAL* 3.8 15.5 - - + +
46A MET* 1.3 80.9 - - - +
48A ALA* 1.3 61.6 + - - +
49A ILE* 3.9 29.2 - - + +
67A ALA* 4.7 4.7 - - + -
68A LYS 3.5 7.4 - - - +
69A TYR* 4.1 9.6 - - + -
77A TRP* 4.6 0.4 - - - -
106A LEU* 4.0 23.1 - - + -
138A VAL* 5.1 0.9 - - + -
151A ILE* 4.2 16.4 - - + -
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Residues in contact with ALA 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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10A LEU* 4.7 0.7 - - + -
11A PHE* 3.5 31.6 - - + -
38A ALA 3.5 4.9 - - - -
39A LEU* 4.3 4.0 - - + -
47A VAL* 1.3 72.1 - - - +
49A ILE* 1.3 61.2 + - - +
66A VAL 3.7 0.5 - - - +
67A ALA* 3.0 5.4 - - - -
68A LYS 2.8 37.2 + - - +
77A TRP* 3.9 22.3 - - + -
355A LEU* 3.8 14.1 - - + -
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Residues in contact with ILE 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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11A PHE* 5.3 0.2 - - - -
36A LEU 3.5 1.4 - - - +
37A PRO* 3.7 0.7 - - - +
38A ALA* 2.8 36.5 + - + +
40A VAL* 5.8 0.7 - - + -
47A VAL* 3.9 20.4 + - + +
48A ALA* 1.3 78.3 - - - +
50A ALA* 1.3 70.0 + - - +
65A THR* 3.8 22.7 - - + -
66A VAL 3.1 2.5 - - - +
67A ALA* 3.8 16.4 - - + -
82A ALA* 5.3 0.4 - - + -
97A PRO* 4.2 11.0 - - + -
99A VAL* 3.9 37.5 - - + -
106A LEU* 4.5 2.2 - - + -
108A VAL* 4.1 8.3 - - + -
153A TRP* 4.0 21.8 - - + -
355A LEU* 4.7 1.1 - - - +
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Residues in contact with ALA 50 (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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11A PHE* 4.6 4.9 - - + -
35A ARG 3.4 12.8 - - - +
36A LEU 3.7 9.4 - - - +
49A ILE* 1.3 81.6 - - - +
51A ASP* 1.4 64.7 + - - +
65A THR* 3.3 9.7 - - - +
66A VAL* 2.6 47.4 + - + -
97A PRO* 4.4 2.9 - - - -
366A LEU* 3.7 24.7 - - + -
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Residues in contact with ASP 51 (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 SER 3.7 0.2 - - - +
34A PHE* 3.1 29.8 - - - +
35A ARG 3.0 13.0 + - - +
36A LEU* 3.0 18.8 - - - +
50A ALA* 1.4 73.3 - - - +
52A ALA* 1.3 58.6 + - - +
53A ARG* 3.0 40.8 + - + +
63A ILE* 3.7 21.7 - - + +
64A ASP 3.8 5.2 - - - -
65A THR* 4.8 1.4 + - - +
66A VAL* 4.3 1.1 - - - -
94A VAL 4.2 2.7 - - - +
95A VAL* 5.1 1.7 - - - +
96A ASP 4.0 3.6 + - - -
97A PRO* 3.3 24.3 - - - +
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Residues in contact with ALA 52 (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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18A VAL* 4.7 0.4 - - + -
31A VAL* 3.9 25.6 - - + -
34A PHE* 4.0 5.6 - - + -
50A ALA 3.7 1.0 + - - -
51A ASP* 1.3 69.4 - - - +
53A ARG* 1.3 62.8 + - - +
54A TYR* 3.3 18.8 + - + -
63A ILE* 3.4 3.0 - - - -
64A ASP 2.9 37.2 + - - +
66A VAL* 4.0 20.6 - - + -
81A ILE* 4.7 5.6 - - + -
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Residues in contact with ARG 53 (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 VAL* 3.8 0.9 - - - +
32A HIS* 3.2 3.1 + - - +
33A SER* 2.8 41.0 + - - +
35A ARG* 4.0 31.4 - - + +
36A LEU* 4.1 11.1 - - - +
51A ASP* 3.0 34.4 + - + +
52A ALA* 1.3 69.9 - - - +
54A TYR* 1.3 67.8 + - - +
55A GLU 3.3 2.9 + - - -
56A THR 3.2 17.9 - - - +
57A SER* 2.7 35.3 + - - +
58A PHE 4.4 0.9 - - - -
59A ASP* 2.6 37.1 + - - +
61A SER* 4.8 0.2 - - - +
62A LEU 3.6 8.1 - - - +
63A ILE* 3.7 23.4 - - + +
96A ASP* 5.4 1.0 + - - -
342A TYR* 6.2 0.4 - - - -
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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