Contacts of the strand formed by residues 7 - 17 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5B LYS* 3.4 37.6 - - + +
6B LEU* 1.3 80.0 - - - +
8B PRO* 1.3 77.1 - - + +
99B GLN* 3.1 8.7 - - - -
100B VAL* 2.7 43.8 + - + +
101B GLY 3.8 10.1 - - - -
103B PRO* 3.5 42.4 - - + -
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Residues in contact with PRO 8 (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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6B LEU 4.6 1.3 - - - +
7B TYR* 1.3 95.6 - - + +
9B LEU* 1.3 68.9 + - - +
98B ILE 3.6 7.2 - - - +
99B GLN* 4.5 8.0 - - + +
107B ARG* 5.0 6.2 + - - -
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Residues in contact with LEU 9 (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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8B PRO* 1.3 80.8 - - - +
10B LYS* 1.3 64.8 + - - +
69B ALA* 3.9 12.3 - - + -
70B VAL 3.3 28.7 - - - +
71B PRO* 3.7 22.7 - - + -
72B GLU* 5.1 3.6 - - - +
97B ASP* 3.9 5.9 - - - +
98B ILE* 2.8 36.8 + - + +
100B VAL* 4.2 24.9 - - + -
103B PRO* 5.5 0.9 - - + +
106B PHE* 3.7 35.4 - - + -
107B ARG* 4.0 19.5 - - - +
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Residues in contact with LYS 10 (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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99A GLN* 4.1 15.5 + - - -
9B LEU* 1.3 78.3 - - - +
11B LYS* 1.3 58.2 + - - +
12B LEU* 4.8 1.1 - - + -
69B ALA* 3.4 4.3 - - - +
70B VAL* 2.7 46.1 + - + +
72B GLU* 3.6 42.2 + - + -
75B VAL* 3.7 28.0 - - + -
95B VAL* 4.3 15.0 - - + +
96B HIS 3.3 10.1 - - - +
97B ASP* 2.5 34.2 + - - +
98B ILE* 4.1 2.5 - - - -
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Residues in contact with LYS 11 (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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10B LYS* 1.3 76.0 - - - +
12B LEU* 1.3 64.8 + - - +
13B GLU* 3.0 35.5 + - - +
67B ILE* 3.6 25.2 - - + +
68B ALA 3.4 12.1 - - - +
69B ALA* 4.2 4.9 - - + +
95B VAL* 3.8 0.5 - - - -
96B HIS* 2.8 52.4 + - + -
98B ILE* 3.8 19.9 - - + +
11C LYS* 5.2 0.2 - - - +
13C GLU* 2.7 38.9 + - - +
94C PHE* 3.7 13.2 - - + -
96C HIS* 3.0 19.8 + - + +
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Residues in contact with LEU 12 (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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10B LYS* 4.8 0.2 - - + -
11B LYS* 1.3 79.8 - - - +
13B GLU* 1.3 61.9 + - - +
14B ILE* 3.9 26.9 - - + -
28B LEU* 5.0 0.2 - - + -
66B ILE 3.3 3.5 - - - +
67B ILE* 3.3 5.4 - - - +
68B ALA* 2.8 40.0 + - + +
70B VAL* 4.3 20.2 - - + -
75B VAL* 4.5 13.5 - - + -
78B LEU* 3.7 34.8 - - + -
79B LEU* 5.1 6.1 - - + -
82B PHE* 5.6 2.0 - - + -
93B VAL* 4.3 17.0 - - + -
94B PHE 3.5 2.7 - - - +
95B VAL* 4.3 19.7 - - + -
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Residues in contact with GLU 13 (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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11A LYS* 2.6 29.1 + - - +
13A GLU* 4.3 2.3 - - - +
67A ILE* 4.7 3.1 - - - +
11B LYS* 3.0 28.9 + - - -
12B LEU* 1.3 77.2 - - - +
14B ILE* 1.3 62.0 + - - +
15B ILE* 4.0 1.9 + - + +
65B MET* 4.0 31.0 - - - +
66B ILE 3.5 3.6 - - - -
67B ILE* 4.6 6.8 - - + +
92B VAL 3.7 1.6 - - - +
93B VAL* 3.3 3.8 - - - +
94B PHE* 2.8 57.0 + - + +
96B HIS* 3.2 18.1 - - + -
13C GLU* 4.2 4.5 - - - +
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Residues in contact with ILE 14 (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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12B LEU* 4.2 26.7 - - + -
13B GLU* 1.3 75.0 - - - +
15B ILE* 1.3 62.6 + - - +
16B LEU* 3.9 19.3 + - + +
28B LEU* 4.3 18.4 - - + -
64B ILE 3.7 1.2 - - - +
65B MET* 3.3 1.8 - - - +
66B ILE* 2.8 54.0 + - + +
68B ALA* 5.0 1.8 - - + -
82B PHE* 3.9 34.1 - - + -
86B PHE* 4.1 22.4 - - + -
92B VAL 3.6 2.9 - - - +
93B VAL* 4.3 14.1 - - + -
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Residues in contact with ILE 15 (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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37A THR* 3.5 31.2 - - + +
67A ILE* 5.3 1.8 - - + -
13B GLU 4.9 1.6 - - - +
14B ILE* 1.3 76.1 - - - +
16B LEU* 1.3 65.8 + - - +
42B LEU* 5.2 0.4 - - + -
63B LEU* 4.7 10.5 - - + -
64B ILE 3.4 11.7 - - - +
65B MET* 3.8 27.1 - - + -
86B PHE* 3.8 1.9 - - - -
91B GLY* 2.8 25.3 - - - -
92B VAL* 2.8 30.6 + - + +
94B PHE* 3.8 29.4 - - + -
201B ADP 3.9 27.4 - - - +
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Residues in contact with LEU 16 (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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14B ILE* 4.1 18.8 - - + +
15B ILE* 1.3 78.6 - - - +
17B GLU* 1.3 85.3 + - - +
20B HIS 4.4 9.9 - - - +
23B PHE* 5.7 0.2 - - + -
24B ALA* 3.8 24.7 - - + -
63B LEU* 3.5 10.7 - - - +
64B ILE* 2.9 54.6 + - + +
66B ILE* 4.6 4.7 - - + -
82B PHE* 4.6 3.8 - - + -
85B PHE* 3.9 30.3 - - + -
86B PHE* 4.4 1.8 - - + -
90B SER 4.0 14.8 - - - +
91B GLY* 4.3 1.8 - - - -
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Residues in contact with GLU 17 (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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16B LEU* 1.3 90.9 - - - +
18B GLY* 1.3 64.9 + - - +
19B ALA* 3.1 2.2 - - + +
20B HIS* 3.1 40.0 + - + +
51B TYR* 4.3 17.5 + - + -
60B ASP 4.0 12.3 - - - +
61B ASP* 5.1 7.8 - - - +
62B ALA 3.6 5.4 - - - +
63B LEU* 4.1 14.4 - - + -
89B HIS* 5.0 1.2 + - - -
90B SER* 4.0 29.6 + - - +
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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