Contacts of the strand formed by residues 63 - 72 (chain A) in PDB entry 3AEV
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 LYS 63 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A VAL* 4.1 10.5 - - + -
17A ALA 3.4 6.5 - - - +
18A THR* 3.0 28.3 + - - +
32A ASP* 2.6 30.4 + - - +
61A GLY 5.0 3.8 - - - -
62A GLN* 1.3 76.7 + - - +
64A VAL* 1.3 65.7 + - - +
90A ARG* 5.0 2.6 + - - -
27B GLU* 2.7 37.7 + - + +
31B PHE* 3.7 25.1 - - + -
32B PHE* 4.2 31.2 - - + -
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Residues in contact with VAL 64 (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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15A VAL 3.6 0.2 - - - +
16A VAL* 3.3 5.2 - - - +
17A ALA* 2.8 35.9 + - + +
19A VAL* 5.1 1.8 - - + -
29A LEU* 4.1 21.8 - - + -
41A MET* 4.6 2.7 - - + -
58A LEU* 4.7 8.1 - - + -
62A GLN* 4.0 22.4 - - + +
63A LYS* 1.3 80.0 - - - +
65A VAL* 1.3 75.1 + - - +
66A ALA* 3.9 14.1 - - + -
82A LEU* 3.8 27.4 - - + -
90A ARG* 5.5 2.0 - - - +
31B PHE* 3.8 5.9 - - - -
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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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14A PHE* 4.4 9.9 - - + -
15A VAL 3.3 6.7 - - - +
16A VAL* 4.7 2.5 - - + -
64A VAL* 1.3 74.7 - - - +
66A ALA* 1.3 63.3 + - - +
82A LEU* 3.2 21.0 - - - +
85A VAL* 3.7 22.4 - - + +
89A GLN 4.9 0.2 - - - +
90A ARG* 4.1 29.9 + - + +
93A LYS* 3.7 33.2 - - + -
94A LEU* 3.8 29.2 - - + -
31B PHE* 4.3 8.2 - - + -
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Residues in contact with ALA 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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14A PHE* 3.4 4.3 - - - -
15A VAL* 2.9 35.7 + - + +
17A ALA* 5.3 0.7 - - + -
41A MET* 4.2 6.5 - - + -
64A VAL* 3.9 15.5 - - + -
65A VAL* 1.3 76.6 - - - +
67A LYS* 1.3 61.9 + - - +
80A LEU* 4.1 30.1 - - + -
81A SER 3.4 12.6 - - - +
82A LEU 4.8 0.2 - - - +
85A VAL* 3.9 5.6 - - - -
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Residues in contact with LYS 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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12A GLY* 4.1 22.0 - - - -
13A GLU 3.6 6.3 - - - +
14A PHE* 3.6 37.6 - - + -
66A ALA* 1.3 75.1 - - - +
68A VAL* 1.3 73.3 + - - +
69A ILE* 3.5 11.8 + - + -
80A LEU* 3.1 7.7 - - - +
81A SER* 2.8 36.7 + - - +
84A ARG* 4.2 29.9 + - + +
85A VAL* 3.8 4.6 - - + +
89A GLN* 5.3 2.2 + - - -
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Residues in contact with VAL 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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9A PRO* 3.9 17.5 - - + -
10A GLU 3.4 26.5 - - - +
11A GLU* 4.1 3.8 - - - +
12A GLY* 2.8 28.6 + - - -
13A GLU 2.8 19.8 + - - +
15A VAL* 3.8 20.9 - - + -
31A LEU* 5.8 0.2 - - + -
67A LYS* 1.3 75.1 - - - +
69A ILE* 1.3 62.0 + - - +
70A ARG 4.0 16.6 - - - +
71A VAL* 4.3 8.5 - - + -
78A ILE* 4.3 6.3 - - + -
79A ASP 3.6 5.2 - - - +
80A LEU* 3.7 17.7 - - + -
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Residues in contact with ILE 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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11A GLU* 3.6 17.9 - - - +
45A GLU* 3.8 19.3 - - + +
67A LYS* 3.5 10.5 + - + +
68A VAL* 1.3 77.9 - - - +
70A ARG* 1.3 63.8 + - + +
79A ASP* 2.9 31.7 + - + +
80A LEU 4.0 11.7 - - - +
81A SER* 3.7 16.4 - - - -
84A ARG* 3.6 49.6 - - - +
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Residues in contact with ARG 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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11A GLU* 3.8 8.7 - - - +
68A VAL* 3.6 4.0 - - - +
69A ILE* 1.3 82.5 - - + +
71A VAL* 1.3 70.6 + - - +
72A ASP* 4.3 21.4 + - - +
77A HIS* 3.8 30.4 + - - +
78A ILE* 3.4 2.0 - - - -
79A ASP* 2.8 68.7 + - + +
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Residues in contact with VAL 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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8A TYR* 4.4 13.9 - - + -
9A PRO* 3.7 20.4 - - + +
10A GLU* 4.7 0.4 - - - -
11A GLU* 3.5 45.1 + - + +
68A VAL* 4.3 6.3 - - + -
70A ARG* 1.3 83.5 - - - +
72A ASP* 1.3 66.4 - - - +
73A PRO* 3.9 13.1 - - + +
77A HIS 3.4 8.5 - - - +
78A ILE* 4.2 13.5 - - + -
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Residues in contact with ASP 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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8A TYR* 5.9 0.2 - - - -
70A ARG* 4.3 15.5 + - - +
71A VAL* 1.3 73.2 - - - +
73A PRO* 1.4 60.0 - - - +
74A ARG* 3.6 9.0 + - - +
75A LYS* 3.4 33.6 + - - +
76A GLY* 2.7 30.8 + - - -
77A HIS* 2.7 34.2 + - + +
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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