Contacts of the strand formed by residues 13 - 20 (chain B) in PDB entry 3OOT
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 GLN 13 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7B THR 3.5 1.4 - - - +
8B ASN* 3.8 1.6 - - - -
9B TYR* 2.8 63.1 + - + +
10B MET* 6.0 0.2 - - - +
11B ASP 3.8 0.2 - - - -
12B THR* 1.4 89.0 + - - +
14B TYR* 1.3 63.3 + - - +
15B TYR* 4.1 7.6 - - + -
30B VAL* 5.4 1.8 - - + -
114B LEU* 3.1 22.2 + - - +
115B ALA* 4.2 0.2 - - - -
116B GLU* 2.6 33.5 + - - +
117B PHE* 3.5 14.4 - - + -
327B SSR 3.5 30.2 - - + -
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Residues in contact with TYR 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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6B LEU* 4.2 10.6 - - + +
7B THR 3.2 5.4 - - - +
8B ASN* 3.5 24.9 - - + -
11B ASP* 3.3 20.3 + - - -
12B THR 4.6 0.7 - - - -
13B GLN* 1.3 76.1 - - - +
15B TYR* 1.3 61.5 + - - +
30B VAL* 3.6 24.0 - - - +
31B PHE* 4.7 1.9 + - - -
155B TYR* 3.6 55.0 + + + -
156B ASN 2.9 19.4 + - - -
162B GLY 3.3 28.5 - - - -
163B GLY* 4.9 1.3 - - - -
216B THR 5.7 0.4 - - - -
303B ALA* 3.8 22.9 - - + -
307B ARG* 2.8 22.7 + - - -
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Residues in contact with TYR 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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253A PRO* 4.3 10.6 - - - +
270A THR* 5.5 4.5 - - + -
272A ALA* 5.6 0.9 - - + +
5B ILE 4.3 0.2 - - - +
6B LEU* 3.3 7.2 - - - +
7B THR* 2.7 68.6 + - + +
9B TYR* 3.8 21.2 - - + +
13B GLN* 4.3 10.8 - - + -
14B TYR* 1.3 76.5 - - - +
16B GLY* 1.3 58.4 + - - +
28B LYS* 3.9 39.6 + - + +
29B VAL 3.2 21.8 - - - +
30B VAL* 4.3 1.1 - - + -
116B GLU* 3.6 38.9 + - + +
117B PHE* 4.1 14.8 - - + -
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Residues in contact with GLY 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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4B VAL* 4.2 1.1 - - - -
5B ILE 3.8 9.9 - - - -
6B LEU* 3.6 18.4 - - - +
15B TYR* 1.3 74.7 - - - +
17B GLU* 1.3 63.9 + - - +
28B LYS* 3.3 8.1 - - - +
29B VAL* 2.9 31.8 + - - -
31B PHE* 4.0 8.9 - - - -
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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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268A THR* 4.7 2.3 - - - +
270A THR* 3.6 26.2 + - + +
273A ASP* 3.8 5.7 - - - +
308A LYS* 2.8 36.2 + - - -
4B VAL* 4.3 15.7 - - - +
5B ILE 4.7 1.8 + - - +
16B GLY* 1.3 78.3 - - - +
18B ILE* 1.3 69.2 + - - +
26B THR* 4.0 21.0 - - + +
27B PHE 3.4 7.2 - - - +
28B LYS* 5.3 4.3 - - + -
90B THR 4.5 1.9 - - - +
91B VAL* 4.9 3.8 - - - +
92B GLY 5.0 2.8 + - - -
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Residues in contact with ILE 18 (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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17B GLU* 1.3 80.6 - - - +
19B GLY* 1.3 58.5 - - - +
20B ILE* 3.9 29.6 - - + -
25B GLN 3.7 0.9 - - - +
26B THR* 3.5 6.1 - - - +
27B PHE* 3.0 33.0 + - + +
29B VAL* 3.8 40.8 - - + -
31B PHE* 4.0 6.3 - - + -
38B VAL* 4.9 3.1 - - + -
40B VAL* 4.8 2.7 - - + -
89B ILE* 4.2 15.7 - - + -
90B THR 3.5 9.0 - - - +
91B VAL* 3.9 29.8 - - + -
121B VAL* 4.1 14.4 - - + -
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Residues in contact with GLY 19 (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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18B ILE* 1.3 74.0 - - - +
20B ILE* 1.3 62.6 + - - +
21B GLY 4.3 0.2 - - - -
24B PRO* 4.1 18.4 - - - -
25B GLN 3.4 7.2 - - - -
26B THR* 4.7 3.1 - - - -
88B ILE 3.7 1.3 - - - +
89B ILE* 3.3 6.4 - - - +
90B THR* 2.8 40.2 + - - -
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Residues in contact with ILE 20 (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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18B ILE* 3.9 20.4 - - + -
19B GLY* 1.3 78.2 - - - +
21B GLY* 1.3 64.0 + - - +
25B GLN* 2.9 38.6 + - - +
27B PHE* 3.8 12.8 - - + -
38B VAL* 5.7 1.3 - - + -
40B VAL* 3.7 41.1 - - + -
56B PHE* 3.7 24.7 - - + -
87B ASP* 4.0 7.2 - - + -
88B ILE 3.5 5.4 - - - +
89B ILE* 4.1 13.7 - - + -
101B PHE* 3.7 28.3 - - + -
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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