Contacts of the strand formed by residues 7 - 17 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5C LYS* 3.7 29.4 - - + +
6C LEU* 1.3 78.3 - - - +
8C PRO* 1.3 75.3 - - + +
9C LEU* 6.2 0.2 - - + -
99C GLN* 3.1 8.3 - - - -
100C VAL* 2.7 54.2 + - + +
101C GLY 3.7 15.9 - - - -
103C PRO* 3.6 37.0 - - + -
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Residues in contact with PRO 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C LEU 4.6 1.8 - - - +
7C TYR* 1.3 92.4 - - + +
9C LEU* 1.3 72.5 + - - +
72C GLU 5.7 0.9 + - - -
98C ILE 3.5 8.1 - - - +
99C GLN* 4.6 5.6 - - + +
107C ARG* 4.8 6.8 + - - -
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Residues in contact with LEU 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C TYR* 6.2 0.4 - - + -
8C PRO* 1.3 80.7 - - - +
10C LYS* 1.3 64.9 + - - +
69C ALA* 3.7 25.4 - - + -
70C VAL 3.5 16.2 - - - +
71C PRO* 4.1 15.0 - - + -
72C GLU* 5.3 2.2 - - - +
97C ASP* 3.8 4.9 - - - +
98C ILE* 2.9 38.0 + - + +
100C VAL* 3.8 28.9 - - + -
103C PRO* 5.4 0.2 - - + -
106C PHE* 3.7 33.0 - - + -
107C ARG* 4.0 24.2 - - - +
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Residues in contact with LYS 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B GLN* 4.2 15.6 + - - -
9C LEU* 1.3 77.5 - - - +
11C LYS* 1.3 61.4 + - - +
12C LEU* 4.2 5.4 - - + -
69C ALA* 3.4 6.2 - - - +
70C VAL* 3.0 41.2 + - + +
72C GLU* 2.9 44.4 + - + -
75C VAL* 3.5 27.8 - - + -
95C VAL* 4.1 14.1 - - + +
96C HIS 3.2 10.8 - - - +
97C ASP* 2.5 35.6 + - - +
98C ILE* 4.0 3.3 - - - +
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Residues in contact with LYS 11 (chain C).
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* 5.3 0.2 - - - +
13A GLU* 2.7 42.1 + - - +
94A PHE* 3.6 22.4 - - + -
96A HIS* 3.3 17.2 + - + +
11B LYS* 5.2 0.2 - - - +
10C LYS* 1.3 74.7 - - - +
12C LEU* 1.3 64.2 + - - +
13C GLU* 3.0 37.8 + - - +
67C ILE* 3.8 22.3 - - + +
68C ALA 3.6 6.5 - - - +
69C ALA* 4.5 0.7 - - - -
94C PHE 3.4 0.2 - - - +
95C VAL 3.8 0.2 - - - -
96C HIS* 2.9 52.4 + - + -
98C ILE* 3.9 20.6 - - + +
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Residues in contact with LEU 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C LYS* 4.6 1.6 - - + -
11C LYS* 1.3 78.1 - - - +
13C GLU* 1.3 62.3 + - - +
14C ILE* 4.0 23.8 - - + -
28C LEU* 5.2 1.8 - - + -
66C ILE 3.4 1.3 - - - +
67C ILE* 3.3 7.1 - - - +
68C ALA* 2.8 41.1 + - + +
70C VAL* 4.2 20.2 - - + -
75C VAL* 4.4 15.7 - - + -
78C LEU* 3.9 35.2 - - + -
79C LEU* 5.1 6.3 - - + -
82C PHE* 5.4 2.9 - - + -
93C VAL* 4.4 17.5 - - + -
94C PHE 3.4 3.1 - - - +
95C VAL* 4.4 18.8 - - + -
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Residues in contact with GLU 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A GLU* 4.4 0.7 - - - +
11B LYS* 2.7 34.1 + - - +
13B GLU* 4.2 3.8 - - - +
67B ILE* 4.7 3.1 - - - +
11C LYS* 3.0 29.3 + - - -
12C LEU* 1.3 74.4 - - - +
14C ILE* 1.3 61.8 + - - +
15C ILE* 4.0 1.5 + - + -
65C MET* 3.9 29.9 - - - +
66C ILE 3.7 3.6 - - - -
67C ILE* 4.7 6.8 - - + +
92C VAL 3.7 1.6 - - - +
93C VAL* 3.4 4.2 - - - -
94C PHE* 2.9 58.5 + - + +
96C HIS* 3.4 15.1 - - + -
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Residues in contact with ILE 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C LEU* 4.4 20.4 - - + -
13C GLU* 1.3 75.3 - - - +
15C ILE* 1.3 63.3 + - - +
16C LEU* 3.9 18.5 + - + +
28C LEU* 4.3 15.7 - - + -
64C ILE 3.8 1.0 - - - +
65C MET* 3.2 3.0 - - - +
66C ILE* 2.8 64.7 + - + +
68C ALA* 5.0 1.6 - - + -
82C PHE* 4.0 31.2 - - + -
86C PHE* 3.8 28.9 - - + -
92C VAL 3.6 2.5 - - - +
93C VAL* 4.4 12.3 - - + -
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Residues in contact with ILE 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B THR* 3.5 31.2 - - + +
67B ILE* 5.2 2.2 - - + -
13C GLU 5.0 1.1 - - - +
14C ILE* 1.3 76.1 - - - +
16C LEU* 1.3 65.5 + - - +
42C LEU* 4.5 0.4 - - + -
63C LEU* 4.1 18.8 - - + -
64C ILE 3.5 9.0 - - - +
65C MET* 3.9 27.6 - - + -
86C PHE* 3.7 1.6 - - - -
91C GLY* 3.0 25.2 - - - -
92C VAL* 2.9 28.1 + - + +
94C PHE* 3.8 29.2 - - + -
201C ADP 4.0 20.0 - - - +
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Residues in contact with LEU 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C ILE* 3.9 24.2 - - + +
15C ILE* 1.3 77.9 - - - +
17C GLU* 1.3 76.5 + - - +
20C HIS 4.6 7.4 - - - +
24C ALA* 4.1 19.3 - - + -
63C LEU* 3.7 9.9 - - - -
64C ILE* 3.0 50.1 + - + +
66C ILE* 4.5 7.2 - - + -
82C PHE* 4.8 1.6 - - + -
85C PHE* 3.4 34.5 - - + -
86C PHE* 4.1 2.0 - - + -
90C SER 4.0 16.2 - - - +
91C GLY* 4.6 1.1 - - - -
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Residues in contact with GLU 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C LEU* 1.3 85.9 - - - +
18C GLY* 1.3 64.3 + - - +
19C ALA* 3.1 8.9 - - + +
20C HIS* 3.0 41.2 + - + +
51C TYR* 2.5 48.8 + - + +
61C ASP* 6.1 1.8 - - - +
62C ALA 3.5 8.7 - - - +
63C LEU* 4.1 1.5 - - + +
89C HIS* 5.4 0.8 + - - -
90C SER* 4.4 14.6 + - - -
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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