Contacts of the strand formed by residues 108 - 112 (chain A) in PDB entry 2GO0
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 CYS 108 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A TRP* 3.2 37.0 - - + -
65A TRP* 3.3 26.0 - - + -
68A LEU 3.4 6.3 - - - -
69A HIS* 4.1 0.9 - - - +
70A ASP* 4.1 3.6 + - - -
106A GLY 3.4 1.6 + - - -
107A HIS* 1.3 81.3 - - - +
109A ALA* 1.3 59.6 + - - +
122A ASP* 3.3 6.4 - - - +
123A TYR 2.8 26.4 + - - +
125A CYS* 2.0 46.4 - - - -
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Residues in contact with ALA 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A TRP* 3.0 14.1 - - - -
66A ILE* 3.1 20.5 + - + +
68A LEU* 2.9 35.7 + - + +
69A HIS* 4.7 0.4 - - - +
70A ASP* 5.9 1.3 - - - +
108A CYS* 1.3 73.6 - - - +
110A SER* 1.3 65.0 + - - +
120A TRP* 4.0 20.4 - - + -
121A LYS 3.3 9.4 - - - +
122A ASP* 5.0 5.4 - - - +
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Residues in contact with SER 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A TYR* 4.7 2.2 - - - -
64A VAL 3.0 22.7 - - - -
65A TRP* 2.6 33.3 - - - -
66A ILE* 4.1 4.5 - - - -
109A ALA* 1.3 72.8 - - - +
111A LEU* 1.3 66.1 + - - +
120A TRP* 3.3 4.9 - - - -
121A LYS* 2.8 31.1 + - - +
123A TYR* 3.4 20.8 - - - +
129A LEU* 4.6 5.2 - - - -
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Residues in contact with LEU 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A VAL* 6.5 0.9 - - + -
47A GLY* 5.2 4.0 - - - +
50A VAL* 4.4 13.9 - - + -
51A SER* 5.1 4.9 - - - -
54A VAL* 4.4 11.7 - - + -
62A SER 4.6 0.2 - - - -
63A TYR* 2.9 31.2 - - - +
64A VAL* 2.7 33.2 + - + +
66A ILE* 3.3 33.2 - - + -
110A SER* 1.3 75.2 - - - +
112A SER* 1.3 59.8 + - - +
117A PHE* 2.9 45.3 - - + +
119A ARG 3.6 3.4 - - - +
120A TRP* 4.2 18.2 - - + +
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Residues in contact with SER 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A TYR* 3.1 35.9 - - - -
96A GLU* 5.0 3.8 + - - -
111A LEU* 1.3 73.7 - - - +
113A ARG* 1.3 64.5 + - - +
114A SER* 2.8 6.8 + - - -
115A THR* 2.9 35.5 + - - +
117A PHE* 3.0 13.3 + - - +
119A ARG* 3.4 12.5 + - - +
121A LYS* 4.5 8.3 - - - -
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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