Contacts of the strand formed by residues 10 - 18 (chain P) in PDB entry 4UJ3
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 10 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8P TYR* 3.2 15.2 - - - -
9P ASP* 1.3 112.9 - - + +
11P LEU* 1.3 60.9 + - - +
12P PHE* 3.7 31.0 - + + -
58P LYS* 5.6 2.0 - - + -
60P ILE* 3.1 25.8 - - + +
61P LYS 3.3 21.1 + - - +
173P TYR* 4.1 29.1 + + - -
176P VAL* 3.9 22.7 - - + -
177P SER* 4.3 12.9 - - - -
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Residues in contact with LEU 11 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8P TYR* 3.5 36.7 - - + +
10P TYR* 1.3 73.6 - - - +
12P PHE* 1.3 69.8 + - - +
13P LYS 4.1 1.3 + - - +
61P LYS* 3.7 21.1 - - + +
63P GLN* 4.1 31.9 - - + +
85P VAL* 5.7 1.7 - - - +
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Residues in contact with PHE 12 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10P TYR* 3.7 32.5 - + + -
11P LEU* 1.3 81.5 - - - +
13P LYS* 1.3 56.4 + - - +
14P VAL* 3.7 2.7 + - + +
60P ILE* 3.6 26.5 - - + -
61P LYS 3.4 9.1 + - - +
62P ALA* 3.6 1.7 - - - +
63P GLN* 2.7 35.1 + - - +
85P VAL* 3.7 17.7 - - + -
169P LEU* 3.9 25.6 - - + -
172P ILE* 3.5 36.1 - - + -
173P TYR* 3.8 24.7 - - + -
176P VAL* 3.9 16.6 - - + -
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Residues in contact with LYS 13 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11P LEU* 4.1 2.8 + - + +
12P PHE* 1.3 72.0 - - - +
14P VAL* 1.3 62.9 + - - +
15P VAL* 4.3 3.6 - - - -
63P GLN* 3.6 11.7 - - - +
65P TRP* 3.7 49.2 - - + +
79P ALA 3.3 12.1 + - - -
80P TYR* 2.9 25.7 + - - +
82P ARG* 2.6 30.5 + - - +
83P GLY* 3.6 14.3 + - - +
84P ALA* 3.3 11.6 - - + +
85P VAL* 2.8 33.0 + - - +
86P GLY 3.3 4.2 + - - -
746R MET* 4.6 2.4 - - - +
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Residues in contact with VAL 14 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12P PHE 4.5 6.7 - - - +
13P LYS* 1.3 79.4 - - - +
15P VAL* 1.3 71.6 + - - +
16P LEU* 5.7 0.2 - - + -
62P ALA* 5.1 3.1 - - + -
63P GLN 2.8 13.2 + - - +
64P ILE* 3.3 12.7 - - + +
65P TRP* 3.0 24.4 + - - +
86P GLY* 3.0 25.8 - - - +
87P ALA 4.0 2.5 - - - +
88P LEU* 4.2 22.2 - - + -
165P PHE* 5.2 6.3 - - + -
168P ILE* 4.5 7.9 - - + -
169P LEU* 4.1 25.8 - - + -
172P ILE* 4.2 8.1 - - + -
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Residues in contact with VAL 15 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13P LYS* 4.3 8.1 - - - -
14P VAL* 1.3 77.8 - - - +
16P LEU* 1.3 57.3 + - - +
17P ILE* 3.9 5.3 + - + -
65P TRP* 3.9 7.0 - - + -
80P TYR* 3.4 48.0 - - + +
81P TYR* 4.1 18.4 - - + -
84P ALA* 3.9 17.3 - - + -
86P GLY 2.8 13.0 + - - +
87P ALA* 3.1 27.1 - - + +
88P LEU 2.7 32.1 + - - -
117P ILE* 4.9 0.4 - - + -
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Residues in contact with LEU 16 (chain P).
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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14P VAL* 5.7 0.2 - - + -
15P VAL* 1.3 72.2 - - - +
17P ILE* 1.3 62.9 + - - +
24P LYS* 3.7 33.6 - - + +
27P LEU* 5.0 7.0 - - + -
28P LEU* 3.7 24.7 - - + -
64P ILE* 3.4 30.7 - - + -
65P TRP 3.2 13.6 + - - +
66P ASP* 4.2 9.2 - - + -
67P THR* 4.9 2.4 + - - +
80P TYR* 2.8 23.2 + - - +
88P LEU* 3.6 40.2 - - + +
90P VAL* 4.9 7.4 - - + -
165P PHE* 4.4 5.4 - - + -
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Residues in contact with ILE 17 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15P VAL* 3.9 9.2 + - + -
16P LEU* 1.3 79.7 - - - +
18P GLY* 1.3 59.4 + - - +
24P LYS* 3.4 11.7 - - - +
80P TYR* 4.2 9.2 - - + -
81P TYR* 3.7 30.3 - - + +
87P ALA* 4.9 2.5 - - + -
88P LEU 3.0 11.1 + - - +
89P LEU* 3.6 34.3 - - + +
90P VAL* 2.9 24.6 + - - +
105P TRP* 3.9 26.0 - - + +
109P LEU* 3.8 31.0 - - + -
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Residues in contact with GLY 18 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17P ILE* 1.3 78.3 - - - +
19P ASP* 1.3 61.8 + - - -
22P VAL* 4.2 0.4 - - - -
24P LYS* 2.7 22.2 + - - +
69P GLY* 3.4 5.7 - - - -
89P LEU* 4.7 0.7 - - - -
90P VAL 3.5 14.8 - - - -
105P TRP* 3.4 33.2 - - - -
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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