Contacts of the strand formed by residues 64 - 73 (chain B) in PDB entry 3MLQ
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 LEU 64 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B ILE 3.7 1.9 - - - +
55B GLU* 3.7 2.6 - - - -
56B GLU 3.0 28.6 + - - +
62B GLY 3.9 11.4 + - - +
63B GLY* 1.3 88.3 - - - +
65B VAL* 1.3 61.9 + - - +
66B LEU 4.1 0.2 - - - -
100B LEU* 3.7 24.2 - - + -
101B ILE 3.5 2.5 - - - -
102B HIS* 3.7 30.3 - - + +
104B ASP* 5.0 0.7 - - - +
359B MET* 4.1 27.0 - - + +
364B PRO* 3.8 36.1 - - + +
367B LEU* 4.5 15.7 - - + -
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Residues in contact with VAL 65 (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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53B PRO* 4.9 4.7 - - + -
54B ILE 3.3 6.3 - - - +
55B GLU* 3.3 39.3 - - + +
64B LEU* 1.3 73.7 - - - +
66B LEU* 1.3 68.4 + - - +
67B ASP* 4.8 10.3 - - + +
99B GLN 3.5 2.9 - - - +
100B LEU* 4.7 1.8 - - - -
101B ILE* 3.0 45.7 + - + +
103B LYS* 3.6 30.5 - - + -
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Residues in contact with LEU 66 (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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52B PHE* 3.7 25.3 - - + -
53B PRO* 3.8 0.2 - - - +
54B ILE* 2.9 46.9 + - + +
64B LEU 4.1 0.6 - - - -
65B VAL* 1.3 72.5 - - - +
67B ASP* 1.3 58.9 + - - +
98B LEU* 4.1 4.5 - - + -
99B GLN 3.6 25.8 - - - +
100B LEU* 3.9 8.1 - - + +
355B VAL* 3.5 27.6 - - + -
359B MET* 3.6 17.4 - - + +
369B PRO* 3.8 25.1 - - + -
372B LEU* 4.8 3.6 - - + -
373B VAL* 4.2 18.4 - - + -
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Residues in contact with ASP 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B PHE* 3.4 14.7 - - - +
53B PRO* 3.8 15.6 - - - +
65B VAL* 4.8 6.7 - - + -
66B LEU* 1.3 75.5 - - - +
68B PHE* 1.3 73.4 + - - +
69B LEU* 4.6 3.8 - - + +
98B LEU* 3.3 8.1 - - - +
99B GLN* 3.0 45.2 + - + +
101B ILE* 4.8 16.3 - - + +
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Residues in contact with PHE 68 (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 GLN* 3.7 33.0 - - - -
48B PHE* 3.5 46.7 - + + -
49B LYS* 5.0 12.1 - - + -
52B PHE* 3.4 33.7 + - + +
67B ASP* 1.3 83.3 + - - +
69B LEU* 1.3 80.2 + - - +
70B GLU* 3.4 32.8 - - - -
71B TYR* 3.7 5.8 - - + -
96B ALA* 4.9 0.7 - - + -
98B LEU* 3.9 17.5 - - + -
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Residues in contact with LEU 69 (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 PRO* 5.5 0.5 - - - +
45B GLN* 5.1 1.6 + - - -
67B ASP* 4.1 6.1 - - + +
68B PHE* 1.3 94.0 - - - +
70B GLU* 1.3 69.9 + - + +
97B ARG* 2.9 55.6 + - + +
98B LEU 4.4 0.4 - - - -
99B GLN* 3.6 45.8 - - + +
110B GLU* 4.7 2.5 - - - +
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Residues in contact with GLU 70 (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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86A LYS* 2.8 29.7 + - - +
36B PRO* 3.4 31.1 - - + +
37B GLU 5.4 0.2 + - - -
45B GLN* 5.7 0.4 - - - +
68B PHE* 3.4 15.6 - - - -
69B LEU* 1.3 91.1 - - + +
71B TYR* 1.3 57.2 + - - +
72B ARG* 2.9 19.9 + - - +
96B ALA* 3.4 2.3 - - - -
97B ARG* 2.5 49.6 + - + +
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Residues in contact with TYR 71 (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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29B ALA 4.9 0.2 + - - -
30B LEU 2.1 34.4 + - - -
31B GLN* 3.6 5.7 + - - +
39B ARG* 2.8 57.3 + - - +
44B ILE* 3.6 19.6 - - + +
45B GLN* 2.9 33.9 + - - +
48B PHE* 3.5 34.3 - + + -
68B PHE* 4.1 1.8 - + + -
70B GLU* 1.3 74.4 - - - +
72B ARG* 1.3 79.3 + - - +
73B ILE* 3.9 13.9 - - + -
94B LEU* 3.7 14.4 - - + -
95B TYR 3.2 13.9 - - - +
96B ALA* 4.1 1.1 - - - +
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Residues in contact with ARG 72 (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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78A PHE* 3.6 25.4 - - + -
82A GLU* 5.5 8.5 - - - +
86A LYS* 3.4 44.8 - - + +
88A LEU* 4.3 3.4 - - + -
35B PRO* 5.8 0.4 - - - +
36B PRO* 3.2 28.5 - - - +
39B ARG* 5.1 4.6 - - - +
70B GLU* 2.9 27.9 + - - +
71B TYR* 1.3 85.3 + - - +
73B ILE* 1.3 65.3 + - - +
93B PRO 4.2 0.4 - - - -
94B LEU* 3.2 5.0 - - - +
95B TYR* 2.8 46.2 + - + +
97B ARG* 5.9 0.2 - - - -
112B GLU* 4.3 5.8 - - - +
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Residues in contact with ILE 73 (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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78A PHE* 4.4 4.0 - - - -
30B LEU* 3.5 37.0 - - + +
32B ALA* 3.2 51.2 + - + +
39B ARG* 4.7 2.2 - - - +
44B ILE* 5.6 0.7 - - + -
71B TYR* 3.9 9.3 - - + -
72B ARG* 1.3 70.5 - - - +
74B GLY* 1.3 68.3 + - - +
75B ASP* 5.3 0.5 - - - +
92B ALA* 4.8 7.9 - - + +
93B PRO 3.2 6.1 - - - +
94B LEU* 3.2 39.5 - - + -
118B LEU* 4.3 11.0 - - + -
120B LEU* 6.1 1.1 - - + -
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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