Contacts of the strand formed by residues 33 - 42 (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 SER 33 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A VAL* 3.6 2.0 - - - +
32A HIS* 1.3 108.0 + - - +
34A PHE* 1.3 64.3 + - - +
35A ARG* 4.3 0.7 - - - -
53A ARG* 2.8 40.6 + - - +
57A SER* 3.6 24.0 - - - -
363A VAL* 3.6 0.2 - - - -
364A TYR* 3.1 30.8 + - - -
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Residues in contact with PHE 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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11A PHE* 3.6 55.0 - + + +
12A LYS 3.9 21.1 - - - -
13A ARG 4.4 0.2 - - - -
16A SER* 3.9 16.2 - - - -
18A VAL* 4.4 7.6 - - + -
31A VAL* 3.2 45.3 - - + -
33A SER* 1.3 73.0 - - - +
35A ARG* 1.3 67.4 + - - +
50A ALA* 5.3 0.2 - - + -
51A ASP 3.1 16.4 - - - +
52A ALA* 4.0 11.7 - - + -
66A VAL* 4.1 7.9 - - + -
68A LYS* 6.1 0.7 - - - -
357A GLU* 4.3 0.7 - - - +
364A TYR* 3.0 25.4 + - - +
365A SER 4.0 0.3 - - - +
366A LEU* 3.7 22.3 - - + +
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Residues in contact with ARG 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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33A SER* 4.3 0.9 - - - -
34A PHE* 1.3 78.5 - - - +
36A LEU* 1.3 67.7 + - + +
37A PRO* 3.5 3.4 - - - -
50A ALA* 3.4 5.4 - - - +
51A ASP* 3.0 28.9 + - + +
53A ARG* 4.0 40.0 - - - +
57A SER* 5.1 2.3 + - - -
59A ASP* 4.4 13.9 + - - -
314A ARG* 3.6 24.7 - - - +
341A ALA* 4.4 1.2 - - - +
342A TYR* 3.8 22.2 + - - -
357A GLU* 2.8 37.3 + - - +
364A TYR* 3.4 49.5 + - + -
366A LEU* 4.3 0.9 - - - -
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Residues in contact with LEU 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 ARG* 1.3 81.3 - - + +
37A PRO* 1.3 74.7 - - - +
38A ALA* 3.5 2.8 + - - +
49A ILE 3.5 9.0 - - - +
50A ALA* 3.7 4.3 - - - -
51A ASP* 3.0 35.9 - - - +
53A ARG* 4.1 8.1 - - - +
95A VAL* 5.7 0.2 - - + -
96A ASP* 3.2 35.0 - - - +
97A PRO* 4.4 11.7 - - + +
179A ALA* 3.7 29.4 - - + -
180A GLY 5.2 1.5 + - - -
230A GLU* 5.4 1.3 - - - +
286A GLN* 5.1 1.1 - - + -
342A TYR* 3.4 32.3 - - + -
357A GLU* 3.0 4.2 + - - -
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Residues in contact with PRO 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 ARG 3.5 3.3 - - - -
36A LEU* 1.3 94.2 - - - +
38A ALA* 1.3 59.6 + - - +
49A ILE 3.7 5.6 - - - +
180A GLY* 3.9 11.4 - - - -
286A GLN* 4.5 3.0 + - - -
342A TYR* 3.5 38.4 - - + +
343A SER* 3.9 6.4 - - - +
344A SER* 3.6 9.5 - - - -
355A LEU* 3.6 41.5 - - + +
357A GLU* 4.0 0.9 - - - +
366A LEU* 3.9 19.1 - - + -
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Residues in contact with ALA 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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36A LEU 4.5 2.5 - - - +
37A PRO* 1.3 75.8 - - - +
39A LEU* 1.3 58.2 + - - +
40A VAL* 5.0 1.6 - - - -
47A VAL 3.7 1.7 - - - +
48A ALA* 3.5 2.4 - - - -
49A ILE* 2.8 43.6 + - + +
97A PRO 4.8 2.0 - - - +
99A VAL* 3.9 20.0 - - + -
180A GLY* 3.7 30.3 - - - +
181A VAL* 4.0 4.5 - - + -
344A SER* 3.6 5.6 - - - -
355A LEU* 4.2 2.3 - - - +
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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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38A ALA* 1.3 71.1 - - - +
40A VAL* 1.3 70.0 + - - +
46A MET* 3.9 20.6 - - + -
47A VAL 3.7 10.3 - - - +
48A ALA* 4.3 13.2 - - + -
77A TRP* 4.6 0.7 - - + -
181A VAL* 4.0 4.5 - - - +
344A SER* 2.8 31.5 + - - +
345A VAL 4.9 1.7 - - - +
346A LEU* 3.7 37.0 - - + +
353A TYR* 3.9 20.0 - - + -
354A CYS 4.3 0.4 - - - +
355A LEU* 3.8 34.1 - - + +
368A PHE* 4.0 10.5 - - + -
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Residues in contact with VAL 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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38A ALA 5.0 1.3 - - - +
39A LEU* 1.3 83.1 - - - +
41A ASN* 1.3 60.3 + - - +
42A VAL* 4.2 2.7 - - + -
46A MET* 3.5 5.7 - - - +
47A VAL* 2.9 46.5 + - + +
49A ILE* 5.8 0.7 - - + -
99A VAL* 4.2 11.7 - - + -
101A VAL* 3.6 30.5 - - + -
106A LEU* 3.9 17.9 - - + -
181A VAL* 3.8 31.0 - - + -
346A LEU* 3.7 12.4 - - - +
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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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40A VAL* 1.3 76.5 - - - +
42A VAL* 1.3 69.6 + - - +
43A ASP* 4.2 2.5 + - - +
44A GLY* 2.7 41.0 + - - +
45A VAL 3.4 4.1 - - - +
46A MET* 4.7 0.2 - - - +
101A VAL* 3.8 16.3 - - - +
346A LEU* 3.5 19.5 - - + +
348A LYS* 3.8 30.0 - - + +
349A ASP* 5.6 0.8 + - - -
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Residues in contact with VAL 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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40A VAL* 4.2 3.1 - - + -
41A ASN* 1.3 76.3 + - - +
43A ASP* 1.3 72.7 + - + +
44A GLY 3.1 0.2 - - - -
45A VAL* 2.9 29.6 + - - +
47A VAL* 4.4 4.9 - - + -
101A VAL* 3.7 17.9 - - + -
103A GLY 3.4 22.4 - - - +
104A ASN* 3.7 17.9 - - - -
106A LEU* 3.5 39.0 - - + -
138A VAL* 3.8 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