Contacts of the strand formed by residues 57 - 64 (chain B) in PDB entry 3MTS
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 GLN 57 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52B LYS 3.8 0.3 - - - +
53B LYS* 3.3 3.3 - - - -
54B ILE 2.9 40.4 + - - +
55B ARG 3.3 0.8 + - - -
56B GLU* 1.3 77.2 - - + +
58B GLU* 1.3 83.0 + - - +
59B TYR* 3.4 34.2 - - + +
76B PRO* 3.3 11.6 - - - +
78B GLN* 2.8 40.1 + - - +
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Residues in contact with GLU 58 (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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51B TYR* 3.0 35.7 + - + +
52B LYS 3.5 4.5 - - - -
53B LYS* 4.2 15.3 + - + +
56B GLU 4.0 5.6 + - - +
57B GLN* 1.3 86.8 + - - +
59B TYR* 1.3 61.9 + - - +
60B TYR* 3.5 14.0 + - + -
76B PRO* 3.4 0.5 - - - +
77B ARG* 2.9 50.8 + - + +
78B GLN* 5.0 1.8 - - - +
90B HIS* 5.3 1.2 + - - -
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Residues in contact with TYR 59 (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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51B TYR* 3.4 6.1 - - - -
52B LYS* 2.7 38.0 + - + +
54B ILE* 4.4 24.5 - - + -
57B GLN* 3.4 34.7 - - + +
58B GLU* 1.3 75.9 - - - +
60B TYR* 1.3 65.9 - - - +
74B TRP* 3.7 24.7 - + + -
75B GLU 3.3 7.9 - - - +
76B PRO* 3.5 38.5 - - + +
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Residues in contact with TYR 60 (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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48B LEU* 4.0 19.3 - - + -
50B ASP 3.3 16.4 - - - +
51B TYR* 3.2 31.6 - + + -
58B GLU* 3.5 18.7 + - + -
59B TYR* 1.3 77.0 - - - +
61B LEU* 1.3 60.4 - - - +
62B VAL* 3.5 2.9 + - - +
73B THR 3.5 1.0 - - - +
74B TRP* 3.5 4.7 - - - -
75B GLU* 2.7 37.6 + - - +
77B ARG* 4.0 22.7 - - + -
80B LEU* 3.8 29.4 - - + -
86B LEU* 3.6 23.1 - - + +
89B PHE* 4.1 8.7 - + - -
90B HIS* 2.5 31.7 + - - -
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Residues in contact with LEU 61 (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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48B LEU* 3.5 4.5 - - - -
49B CYS* 2.8 42.5 + - + +
50B ASP* 3.1 36.9 + - + +
60B TYR* 1.3 70.7 - - - +
62B VAL* 1.3 58.7 + - - +
72B SER* 3.7 31.4 - - - +
73B THR* 3.6 21.8 - - - -
74B TRP* 3.5 31.6 - - + +
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Residues in contact with VAL 62 (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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45B VAL* 4.0 15.0 - - + -
47B TYR 3.9 2.5 - - - -
48B LEU* 3.8 19.5 - - + -
49B CYS* 4.8 0.2 - - - -
60B TYR 3.9 4.9 - - - +
61B LEU* 1.3 73.7 - - - +
63B LYS* 1.3 74.5 + - - +
64B TRP* 3.5 39.0 + - + -
72B SER* 3.3 24.7 - - - -
73B THR 2.8 17.3 + - - +
75B GLU* 3.7 22.4 - - + -
80B LEU* 4.0 15.3 - - + -
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Residues in contact with LYS 63 (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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46B GLU* 2.8 53.1 + - + +
47B TYR* 2.8 62.1 + - + +
49B CYS* 4.0 4.1 - - - -
61B LEU 3.9 1.4 + - - -
62B VAL* 1.3 74.2 - - - +
64B TRP* 1.3 65.6 + - - +
66B GLY 4.5 2.2 - - - +
67B TYR 2.6 33.2 + - - +
68B PRO* 4.2 1.8 - - - +
69B ASP* 4.0 28.9 - - + +
72B SER* 3.6 9.4 + - - +
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Residues in contact with TRP 64 (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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43B GLY* 3.4 44.6 - - - -
44B GLU 3.5 14.1 - - - +
45B VAL* 4.0 17.7 - - + -
46B GLU* 4.1 1.6 - - - -
62B VAL* 3.5 27.6 + - + -
63B LYS* 1.3 93.3 + - - +
65B ARG* 1.3 66.1 + - - +
67B TYR* 3.4 30.7 + + + +
71B GLU* 3.9 18.1 - - + -
72B SER* 5.5 0.4 - - - +
73B THR* 2.8 21.4 + - + +
75B GLU* 3.6 37.5 - - + -
80B LEU* 5.3 3.1 - - + -
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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