Contacts of the strand formed by residues 8 - 18 (chain C) in PDB entry 4X6D
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 8 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7C PRO* 1.3 76.4 - - - +
9C SER* 1.3 56.1 + - - +
10C PHE 4.2 0.7 - - - -
32C LEU* 4.5 13.5 - - + -
33C SER* 3.9 7.4 - - - +
103C GLU* 3.3 1.4 - - - +
104C LEU* 2.7 46.8 + - + +
106C SER 4.8 13.0 - - - +
170C ILE* 4.1 5.7 - - + +
174C LEU* 3.7 31.6 - - + -
181C LEU* 6.2 1.3 - - + -
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Residues in contact with SER 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 PRO* 3.4 9.5 + - - -
8C LEU* 1.3 74.7 - - - +
10C PHE* 1.3 58.6 + - - +
11C HIS* 3.1 21.7 + - - -
32C LEU* 4.3 2.2 - - - +
33C SER* 3.2 24.2 + - - -
102C CYS 3.7 4.3 - - - -
103C GLU* 3.3 30.1 + - - +
113C PHE* 3.7 17.2 - - - -
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Residues in contact with PHE 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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9C SER* 1.3 71.2 - - - +
11C HIS* 1.3 58.2 + - - +
12C VAL* 4.0 26.9 - - + -
30C GLY* 4.3 4.0 - - - -
31C TRP 3.0 30.3 - - - -
32C LEU* 4.0 10.5 - - + +
37C THR* 3.5 22.4 - - - -
38C HIS* 4.0 11.7 - + - -
101C GLY* 3.2 21.8 - - - -
102C CYS 3.1 12.5 + - - -
166C CYS* 4.2 14.6 - - - -
169C PHE* 3.5 33.7 - + - -
170C ILE* 3.6 28.8 - - + +
173C LEU* 4.1 16.8 - - + -
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Residues in contact with HIS 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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9C SER* 3.1 18.9 + - - -
10C PHE* 1.3 74.8 - - - +
12C VAL* 1.3 62.6 + - - +
13C ILE* 3.5 18.1 - - + +
30C GLY* 3.5 1.4 - - - -
31C TRP* 2.8 51.6 + + + +
33C SER* 3.3 27.7 + - - -
99C THR* 3.5 31.4 - - + -
100C GLY 3.1 11.4 - - - +
113C PHE* 3.7 12.8 - + + -
55D SER* 4.8 6.5 + - - -
56D PHE* 5.3 5.5 + + - -
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Residues in contact with VAL 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 PHE* 4.0 23.6 - - + -
11C HIS* 1.3 76.3 - - - +
13C ILE* 1.3 65.2 + - - +
14C TRP* 3.7 35.0 - - + -
28C VAL* 4.5 9.6 - - + -
29C SER 3.3 14.4 - - - +
30C GLY* 4.5 3.4 - - - -
70C PHE* 4.8 16.2 - - + -
98C VAL 3.6 0.5 - - - +
99C THR* 3.5 4.2 - - - -
100C GLY* 2.7 36.1 + - - +
101C GLY* 6.1 0.2 - - - -
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Residues in contact with ILE 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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11C HIS* 3.5 27.1 - - + +
12C VAL* 1.3 78.2 - - - +
14C TRP* 1.3 64.2 + - - +
15C ILE* 4.8 4.9 - - + -
27C LEU 3.5 1.4 - - - +
28C VAL* 3.4 7.8 - - - +
29C SER* 2.8 35.7 + - - +
31C TRP* 3.3 29.4 - - + +
98C VAL 3.1 4.9 - - - +
99C THR* 3.7 11.2 - - + -
54D LEU 3.8 20.4 - - - +
55D SER* 3.9 15.9 - - - +
56D PHE* 3.8 26.5 - - + +
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Residues in contact with TRP 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 VAL* 3.7 28.5 - - + -
13C ILE* 1.3 78.4 - - - +
15C ILE* 1.3 64.9 + - - +
16C ALA* 4.1 2.0 - - + -
26C ASN* 4.2 10.5 - - - -
27C LEU 3.3 2.7 - - - -
28C VAL* 3.4 29.6 - - + +
70C PHE* 3.6 38.4 - + - -
74C THR* 3.8 23.5 + - + +
96C ILE 3.6 1.2 - - - +
97C GLN* 3.2 6.9 - - - +
98C VAL* 3.0 66.2 + - + +
100C GLY* 4.9 5.8 - - - -
114C LEU* 5.4 2.5 - - + -
56D PHE* 4.2 1.3 - - - -
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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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13C ILE* 4.8 6.3 - - + -
14C TRP* 1.3 79.5 - - - +
16C ALA* 1.3 63.8 + - - +
17C SER* 4.0 14.5 + - - +
25C GLN 3.4 6.2 - - - +
26C ASN* 3.9 2.3 - - - +
27C LEU* 3.0 51.7 + - + +
95C GLU* 5.2 2.5 - - + +
96C ILE 3.6 1.3 - - - +
97C GLN* 4.4 5.6 - - + -
33D SER* 4.7 3.6 - - - +
54D LEU* 3.5 43.3 - - + +
56D PHE* 3.8 19.7 - - + -
62D PHE* 3.6 31.6 - - + -
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Residues in contact with ALA 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 TRP* 5.7 2.0 - - + -
15C ILE* 1.3 72.5 - - - +
17C SER* 1.3 63.5 + - - +
18C PHE* 4.4 21.2 - - + -
25C GLN 3.5 7.9 - - - +
26C ASN* 5.3 1.1 - - - +
78C PHE* 4.7 8.5 - - + -
81C ILE* 6.3 0.4 - - + -
94C PHE 3.9 0.9 - - - +
95C GLU* 3.2 5.1 - - - -
96C ILE* 2.8 53.9 + - + +
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Residues in contact with SER 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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15C ILE* 4.0 7.9 + - - +
16C ALA* 1.3 72.1 - - - +
18C PHE* 1.3 71.0 + - - +
19C TYR 4.0 2.9 - - - -
23C TRP* 3.9 1.7 - - - +
24C LYS* 3.5 2.9 - - - -
25C GLN* 3.2 42.2 + - - +
27C LEU* 5.7 0.9 - - - +
95C GLU* 3.2 34.0 + - - +
33D SER* 3.8 7.4 + - - -
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Residues in contact with PHE 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C ALA* 4.4 16.6 - - + -
17C SER* 1.3 90.6 - - - +
19C TYR* 1.3 54.9 + - - +
20C ASN 3.4 5.4 - - - +
23C TRP 3.7 4.9 - - - +
24C LYS* 3.6 25.1 - - + -
78C PHE* 3.5 42.4 - + - -
81C ILE* 3.8 38.8 - - + -
82C ARG* 5.8 2.2 - - - -
85C ALA* 6.3 0.2 - - + -
92C TYR 2.7 25.4 - - - +
94C PHE* 2.9 60.7 + + + +
95C GLU* 4.6 0.6 - - - +
96C ILE* 5.0 0.4 - - + -
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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