Contacts of the strand formed by residues 116 - 120 (chain B) in PDB entry 3GSB
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 MET 116 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A GLN 4.3 7.2 - - - +
21A LYS* 3.9 22.0 - - - +
22A LEU 3.3 22.0 - - - +
23A MET* 3.9 7.4 - - - +
24A PRO* 4.0 21.8 - - + -
108B ASN* 4.1 1.6 - - - +
114B ILE* 3.5 1.0 - - - +
115B GLU* 1.3 80.6 - - - +
117B VAL* 1.3 62.7 + - - +
285B GLY* 3.0 23.0 - - - -
286B GLY 3.3 6.3 + - - +
288B ARG* 3.5 37.0 - - + +
291B MET* 3.5 27.9 - - + +
292B GLN* 3.8 20.4 - - - +
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Residues in contact with VAL 117 (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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22A LEU 3.2 5.9 + - - +
23A MET* 3.4 27.0 - - - +
24A PRO* 3.4 4.0 - - - +
104B ALA* 3.9 28.0 - - + +
107B VAL* 3.8 18.4 - - + -
108B ASN* 3.6 13.9 - - - +
114B ILE* 3.2 34.8 - - + -
116B MET* 1.3 70.1 - - - +
118B ARG* 1.3 64.1 + - - +
119B PHE* 4.3 14.6 - - + -
283B ALA* 5.2 5.6 - - + -
284B TYR 3.6 6.3 - - - +
285B GLY* 4.1 4.3 - - - +
291B MET* 4.2 0.9 - - - -
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Residues in contact with ARG 118 (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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23A MET* 5.4 1.8 - - - +
24A PRO* 3.2 34.1 + - + +
27A VAL* 2.9 29.2 + - - +
28A SER* 3.5 24.4 + - - +
30A PRO* 4.2 2.6 - - - +
117B VAL* 1.3 76.4 - - - +
119B PHE* 1.3 70.7 + - - +
283B ALA* 3.2 3.9 - - - -
284B TYR* 3.0 58.4 + - + +
291B MET* 4.2 6.1 - - + -
294B VAL* 3.8 7.9 - - + +
295B ALA 3.3 24.8 + - - -
296B PRO* 4.3 2.0 - - - +
302B GLN* 2.9 50.0 + - - +
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Residues in contact with PHE 119 (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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23A MET* 4.5 9.9 - - - -
28A SER* 3.9 21.3 + - - +
100B GLU* 3.7 13.2 - - + -
103B LEU* 3.6 29.2 - - + -
104B ALA* 3.7 25.6 - - + -
107B VAL* 4.9 3.8 - - + -
117B VAL* 4.3 11.4 - - + -
118B ARG* 1.3 86.8 - - - +
120B VAL* 1.3 66.8 + - - +
275B ILE* 4.0 16.2 - - + -
281B VAL* 5.3 5.6 - - + -
282B GLY 3.5 5.2 - - - +
283B ALA* 3.6 17.3 - - + -
302B GLN* 4.7 0.2 + - - -
307B SER* 3.8 14.6 + - - -
308B GLY* 4.4 11.7 - - - +
313B MET* 3.3 29.8 - - + -
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Residues in contact with VAL 120 (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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118B ARG* 4.3 0.2 - - + -
119B PHE* 1.3 80.8 - - - +
121B ASN* 1.3 69.4 + - - +
122B SER 3.3 22.7 - - - +
125B GLU* 3.5 15.0 - - + +
126B ALA* 3.7 13.5 - - + +
281B VAL* 3.6 5.5 - - - +
282B GLY 2.7 36.9 + - - +
283B ALA* 3.8 3.6 - - - +
284B TYR* 3.7 23.6 - - + -
302B GLN* 3.5 25.6 - - + +
307B SER* 3.8 10.5 - - - -
308B GLY 5.4 0.7 + - - -
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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