Contacts of the strand formed by residues 64 - 73 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A ILE 3.7 2.2 - - - +
55A GLU* 3.3 7.2 - - - +
56A GLU* 3.0 30.4 + - + +
63A GLY* 1.3 98.6 - - - +
65A VAL* 1.3 64.3 + - - +
66A LEU 4.2 0.4 - - - -
100A LEU* 3.3 32.1 - - + -
101A ILE 3.5 6.1 - - - +
102A HIS* 3.1 39.9 - - + +
103A LYS* 5.0 0.4 - - - -
104A ASP* 6.5 0.2 - - + -
359A MET* 4.2 29.2 - - + +
364A PRO* 4.0 25.4 - - + +
367A LEU* 4.7 7.2 - - + -
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Residues in contact with VAL 65 (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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53A PRO* 4.2 22.4 - - + -
54A ILE 3.8 2.9 - - - -
55A GLU* 3.6 25.8 - - + +
64A LEU* 1.3 72.4 - - - +
66A LEU* 1.3 62.8 + - - +
67A ASP* 4.7 5.4 - - + +
99A GLN 3.6 1.9 - - - +
100A LEU* 3.7 2.5 - - - +
101A ILE* 2.8 57.6 + - + +
103A LYS* 3.6 32.3 - - + +
344E LEU* 6.0 0.9 - - + -
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Residues in contact with LEU 66 (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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52A PHE* 3.7 29.3 - - + -
53A PRO* 3.2 6.7 - - - +
54A ILE* 3.1 32.9 + - + +
64A LEU 4.2 0.2 - - - -
65A VAL* 1.3 71.6 - - - +
67A ASP* 1.3 57.7 + - - +
98A LEU* 4.4 13.9 - - + -
99A GLN 3.3 23.8 - - - +
100A LEU* 4.0 16.6 - - + -
355A VAL* 3.6 28.3 - - + -
359A MET* 3.8 13.9 - - + -
369A PRO* 4.1 20.4 - - + -
372A LEU* 4.4 3.4 - - + -
373A VAL* 4.6 7.6 - - + -
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Residues in contact with ASP 67 (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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52A PHE* 3.5 20.2 - - - +
53A PRO* 3.5 14.4 - - + +
65A VAL* 4.0 7.5 - - + +
66A LEU* 1.3 74.9 - - - +
68A PHE* 1.3 79.8 + - - +
69A LEU* 5.4 2.1 - - - +
98A LEU* 3.8 8.8 - - - +
99A GLN* 3.1 48.7 + - + +
101A ILE* 5.5 5.8 - - + -
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Residues in contact with PHE 68 (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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45A GLN* 3.5 36.1 - - - -
48A PHE* 3.5 46.9 - + + +
49A LYS* 4.4 16.2 - - + -
52A PHE* 3.7 27.8 - - + +
67A ASP* 1.3 91.5 + - - +
69A LEU* 1.3 75.9 + - - +
70A GLU* 3.4 35.0 - - - -
71A TYR* 3.7 5.8 - + + -
96A ALA* 5.0 0.9 - - + -
97A ARG 4.3 2.2 - - - -
98A LEU* 4.3 11.2 - - + -
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Residues in contact with LEU 69 (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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45A GLN* 5.4 0.9 + - - -
67A ASP* 5.4 2.0 - - - +
68A PHE* 1.3 90.3 - - - +
70A GLU* 1.3 66.7 + - + +
97A ARG* 3.3 44.6 + - + +
99A GLN* 3.7 45.3 - - + +
110A GLU* 4.3 12.8 - - + +
341E ARG* 4.5 5.2 - - - +
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Residues in contact with GLU 70 (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 PRO* 3.0 36.2 - - + +
39A ARG* 5.3 0.7 - - - +
68A PHE* 3.4 20.1 - - - -
69A LEU* 1.3 83.3 - - + +
71A TYR* 1.3 59.5 + - - +
72A ARG* 3.1 35.7 + - - -
96A ALA* 3.6 0.7 - - - -
97A ARG* 2.9 57.3 + - + -
112A GLU* 3.9 4.0 - - - +
86B LYS* 3.7 14.8 + - - +
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Residues in contact with TYR 71 (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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29A ALA 4.5 0.3 + - - -
30A LEU* 2.5 30.6 + - - -
31A GLN* 3.8 7.1 + - - +
39A ARG* 2.9 64.2 + - - +
44A ILE* 4.0 15.2 - - + +
45A GLN* 3.1 39.2 + - - -
48A PHE* 3.8 31.9 - + + -
68A PHE* 4.0 2.9 - + + -
70A GLU* 1.3 77.3 - - - +
72A ARG* 1.3 70.8 + - - +
73A ILE* 3.8 15.9 - - + -
94A LEU* 3.9 14.6 - - + -
95A TYR 3.3 11.4 - - - +
96A ALA* 4.3 1.3 - - - +
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Residues in contact with ARG 72 (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 PRO* 3.3 35.1 - - - +
39A ARG* 5.5 1.1 - - - +
70A GLU* 3.1 21.8 + - + +
71A TYR* 1.3 77.4 + - - +
73A ILE* 1.3 62.9 + - - +
74A GLY 3.9 0.3 + - - -
93A PRO 3.7 0.5 - - - +
94A LEU* 3.5 4.4 - - - +
95A TYR* 2.8 38.6 + - + +
112A GLU* 3.4 26.7 - - - +
78B PHE* 3.7 22.9 - - + -
82B GLU* 3.7 22.2 + - - +
86B LYS* 3.2 44.9 - - - +
88B LEU* 4.1 9.2 - - + +
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Residues in contact with ILE 73 (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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30A LEU* 3.9 27.6 - - + +
32A ALA* 4.1 32.5 + - + +
39A ARG* 5.1 2.4 - - - +
44A ILE* 4.6 0.9 - - + -
71A TYR* 3.8 22.5 + - + -
72A ARG* 1.3 73.2 + - - +
74A GLY* 1.3 80.4 + - - +
75A ASP* 3.8 6.6 - - - +
92A ALA* 3.5 17.7 - - + +
93A PRO 3.5 5.4 - - - +
94A LEU* 3.9 6.7 - - + -
118A LEU* 3.4 32.8 - - + -
120A LEU* 5.0 4.5 - - + -
78B PHE* 3.6 8.0 - - - -
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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