Contacts of the strand formed by residues 8 - 15 (chain B) in PDB entry 5T4S
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 SER 8 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A GLU* 3.6 4.5 - - - -
340A ARG* 4.3 0.7 - - - -
7B THR* 1.3 76.6 - - - +
9B SER* 1.3 58.9 + - - +
10B VAL* 5.2 1.2 - - - +
99B VAL 3.1 11.4 + - - -
100B GLY* 3.3 4.0 - - - -
101B GLY* 2.9 31.0 + - - -
102B ILE* 3.6 24.7 - - - -
176B ILE 3.8 0.5 - - - +
177B VAL* 3.5 1.5 - - - -
178B LEU* 2.6 52.0 + - - +
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Residues in contact with SER 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A GLU* 2.5 34.9 + - - +
338A LEU* 5.1 0.3 - - - +
340A ARG* 3.3 37.8 + - - +
8B SER* 1.3 75.3 - - - +
10B VAL* 1.3 66.0 + - - +
11B ILE* 4.2 3.9 + - - +
100B GLY* 3.8 1.4 - - - -
175B GLN* 3.8 25.8 + - - -
176B ILE 3.1 10.8 - - - -
177B VAL* 4.2 8.1 - - - +
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Residues in contact with VAL 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B SER* 5.2 2.5 - - - +
9B SER* 1.3 78.8 - - - +
11B ILE* 1.3 74.0 + - - +
12B LEU* 3.6 1.3 + - + +
22B GLY* 4.0 6.1 - - - -
23B GLU* 3.8 28.3 - - + +
37B PHE* 4.0 9.6 - - + -
99B VAL* 3.7 30.1 - - + -
100B GLY* 3.8 13.5 - - - +
175B GLN* 3.4 5.7 - - - -
176B ILE* 2.8 51.0 + - + +
178B LEU* 5.6 2.7 - - + -
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Residues in contact with ILE 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A ARG* 3.7 45.5 - - - +
338A LEU* 6.4 1.3 - - + -
339A ALA 4.8 10.1 - - - +
340A ARG* 4.8 17.3 - - - -
9B SER* 5.3 2.9 - - - +
10B VAL* 1.3 76.1 - - - +
12B LEU* 1.3 69.7 + - - +
22B GLY* 3.6 15.8 - - - -
23B GLU* 4.6 5.0 + - - +
172B LEU* 4.0 26.2 - - + -
174B GLY 3.6 7.9 - - - +
175B GLN* 4.6 15.3 - - + +
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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
----------------------------------------------------------
10B VAL* 3.7 13.0 - - + +
11B ILE* 1.3 78.3 - - - +
13B THR* 1.3 63.2 + - - +
20B TYR* 4.5 6.5 - - + -
21B TYR* 3.4 9.4 - - - +
22B GLY* 3.7 24.9 - - - +
37B PHE* 3.9 11.2 - - + -
160B PHE* 4.8 6.5 - - + -
161B TYR 3.9 1.3 - - - +
162B TYR* 3.6 33.2 - - + -
173B GLY 3.2 9.9 + - - -
174B GLY* 2.7 39.7 + - - -
175B GLN 3.7 20.4 - - - +
176B ILE* 3.9 16.2 - - + +
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Residues in contact with THR 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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280A THR* 5.0 1.7 + - - -
282A ALA* 3.2 32.6 - - + +
290A TYR* 5.9 0.4 - - - +
11B ILE 4.2 0.4 + - - -
12B LEU* 1.3 71.5 - - - +
14B ASN* 1.3 68.3 + - - +
15B TYR* 3.7 0.8 + - + -
19B GLN 3.3 2.6 - - - +
20B TYR* 3.3 7.6 - - - -
21B TYR* 2.8 70.1 + - + +
173B GLY* 4.3 1.6 - - - +
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Residues in contact with ASN 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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290A TYR* 3.2 13.7 + - - -
13B THR* 1.3 75.8 - - - +
15B TYR* 1.3 60.9 + - - +
16B MET 3.6 0.5 + - - -
17B ASP* 2.8 52.0 + - - -
19B GLN 3.7 2.9 - - - -
20B TYR* 3.1 17.3 + - + -
163B ASN* 2.9 21.8 + - - +
164B ARG 3.7 2.8 + - - -
165B ASP* 3.6 20.3 - - - +
173B GLY* 3.5 25.0 - - - -
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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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263A PRO* 4.0 15.5 - - + -
290A TYR* 3.7 32.5 - + - -
13B THR* 3.7 2.5 + - + -
14B ASN* 1.3 70.0 - - - +
16B MET* 1.3 95.4 + - + +
17B ASP 3.2 2.2 - - - -
18B THR* 3.0 7.2 + - - -
19B GLN* 2.8 65.0 + - + +
21B TYR* 3.7 21.8 - - + +
121B LEU 4.9 0.9 - - - -
123B GLU* 3.4 43.8 + - + -
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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