Contacts of the strand formed by residues 7 - 17 (chain A) in PDB entry 5D4P
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 TYR 7 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A LYS* 3.6 51.4 + - + +
6A LEU* 1.3 76.5 - - - +
8A PRO* 1.3 74.9 - - + +
99A GLN* 3.2 8.1 - - - -
100A VAL* 2.8 49.1 + - + +
101A GLY 3.7 10.8 - - - -
103A PRO* 3.5 45.9 - - + +
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Residues in contact with PRO 8 (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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6A LEU 4.5 1.8 - - - +
7A TYR* 1.3 96.0 - - + +
9A LEU* 1.3 68.6 + - - +
98A ILE 3.7 7.4 - - - +
99A GLN* 4.7 6.3 - - + +
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Residues in contact with LEU 9 (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 PRO* 1.3 79.8 - - - +
10A LYS* 1.3 64.1 + - - +
69A ALA* 3.8 24.9 - - + -
70A VAL 3.6 7.2 - - - +
71A PRO* 3.5 35.7 - - + -
72A GLU* 4.9 2.2 - - - +
97A ASP* 3.8 4.9 - - - +
98A ILE* 2.9 42.4 + - + +
100A VAL* 4.0 24.7 - - + -
103A PRO* 5.9 3.1 - - + +
106A PHE* 3.7 33.9 - - + -
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Residues in contact with LYS 10 (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 LEU* 1.3 78.9 - - - +
11A LYS* 1.3 61.6 + - - +
12A LEU* 5.0 0.4 - - + -
69A ALA* 3.3 5.2 - - - +
70A VAL* 2.7 39.8 + - + +
72A GLU* 3.4 46.4 + - + -
75A VAL* 3.8 27.6 - - + -
95A VAL* 4.4 13.7 - - + +
96A HIS 3.3 8.5 - - - +
97A ASP* 2.4 39.3 + - - +
98A ILE* 4.2 2.0 - - - -
99C GLN* 4.5 11.9 + - - -
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Residues in contact with LYS 11 (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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10A LYS* 1.3 74.8 - - - +
12A LEU* 1.3 64.5 + - - +
13A GLU* 3.2 34.4 + - - -
67A ILE* 3.6 25.0 - - + +
68A ALA 3.5 10.3 - - - +
69A ALA* 4.2 6.1 - - + +
95A VAL 3.7 0.2 - - - -
96A HIS* 2.8 55.7 + - + -
98A ILE* 3.9 20.4 - - + +
13B GLU* 2.6 29.7 + - - -
94B PHE* 3.7 19.3 - - + -
96B HIS* 2.9 23.3 + - - +
11C LYS* 5.3 0.2 - - - +
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Residues in contact with LEU 12 (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 LYS* 1.3 79.9 - - - +
13A GLU* 1.3 62.4 + - - +
14A ILE* 4.0 25.4 - - + -
28A LEU* 5.1 2.0 - - + -
66A ILE 3.4 0.7 - - - +
67A ILE* 3.2 6.9 - - - +
68A ALA* 2.8 43.5 + - + +
70A VAL* 4.5 8.7 - - + -
75A VAL* 4.4 18.6 - - + -
78A LEU* 4.1 34.5 - - + -
79A LEU* 5.3 6.1 - - + -
82A PHE* 5.3 2.7 - - + -
93A VAL* 4.1 19.5 - - + -
94A PHE 3.3 2.5 - - - +
95A VAL* 4.1 24.9 - - + -
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Residues in contact with GLU 13 (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 LYS* 3.2 26.0 + - - -
12A LEU* 1.3 77.0 - - - +
14A ILE* 1.3 60.1 + - - +
15A ILE* 4.0 2.4 - - + +
65A MET* 4.1 29.1 - - - +
66A ILE 3.3 4.0 - - - -
67A ILE* 4.3 9.8 - - + +
92A VAL 3.7 1.6 - - - +
93A VAL* 3.3 4.5 - - - +
94A PHE* 2.8 57.5 + - + -
96A HIS* 3.1 19.0 - - + -
13B GLU* 4.3 3.5 - - - +
11C LYS* 2.7 33.1 + - - +
13C GLU* 4.4 1.0 - - - +
67C ILE* 5.2 0.5 - - - +
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Residues in contact with ILE 14 (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 LEU* 4.2 22.2 - - + -
13A GLU* 1.3 75.9 - - - +
15A ILE* 1.3 61.6 + - - +
16A LEU* 3.9 13.0 + - + +
28A LEU* 4.2 17.0 - - + -
64A ILE 3.7 1.2 - - - +
65A MET* 3.4 2.3 - - - +
66A ILE* 2.8 61.2 + - + +
68A ALA* 4.9 1.8 - - + -
82A PHE* 3.9 39.3 - - + -
86A PHE* 3.9 26.0 - - + -
92A VAL 3.7 2.5 - - - -
93A VAL* 4.3 12.1 - - + +
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Residues in contact with ILE 15 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A GLU 5.1 1.1 - - - -
14A ILE* 1.3 73.3 - - - +
16A LEU* 1.3 66.3 + - - +
42A LEU* 5.1 0.2 - - + -
63A LEU* 4.2 13.9 - - + -
64A ILE 3.3 9.2 - - - +
65A MET* 3.9 30.1 - - + -
86A PHE* 3.7 2.1 - - - -
91A GLY* 3.0 25.3 - - - -
92A VAL* 2.9 28.6 + - + +
94A PHE* 3.9 27.8 - - + -
201A ADP 3.8 27.4 - - - +
37C THR* 3.5 30.1 - - + +
67C ILE* 5.3 1.8 - - + -
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Residues in contact with LEU 16 (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 ILE* 4.1 20.6 - - + +
15A ILE* 1.3 79.7 - - - +
17A GLU* 1.3 73.9 + - - +
20A HIS 4.6 10.8 - - - +
23A PHE* 5.7 0.4 - - + -
24A ALA* 4.1 20.9 - - + -
63A LEU* 3.6 9.4 - - - -
64A ILE* 2.7 59.4 + - + +
66A ILE* 4.8 5.6 - - + -
82A PHE* 4.6 2.2 - - + -
85A PHE* 3.7 29.8 - - + -
86A PHE* 4.2 4.3 - - + -
90A SER 4.1 15.7 - - - +
91A GLY* 4.5 1.1 - - - -
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Residues in contact with GLU 17 (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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16A LEU* 1.3 87.8 - - - +
18A GLY* 1.3 65.5 + - - +
19A ALA* 3.1 6.7 - - + +
20A HIS* 3.1 41.8 + - + +
51A TYR* 3.6 38.2 + - + +
62A ALA 3.2 10.8 - - - +
63A LEU* 4.4 3.1 - - + +
89A HIS* 4.5 7.8 - - - +
90A SER* 4.6 16.8 + - - +
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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