Contacts of the strand formed by residues 121 - 126 (chain A) in PDB entry 2G5N
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 121 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A GLY 3.4 7.3 + - - -
120A THR* 1.3 83.7 - - - +
122A CYS* 1.3 66.2 + - - +
145A LYS* 3.8 28.8 - - - +
146A ALA* 3.5 7.8 + - - +
147A PRO* 3.5 37.9 - - - +
171A TYR* 3.5 11.6 + - - -
189A CYS* 3.8 7.4 - - - +
190A SER 4.5 2.8 + - - -
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Residues in contact with CYS 122 (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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120A THR 3.8 2.0 - - - -
121A GLN* 1.3 76.3 - - - +
123A LEU* 1.3 61.6 + - - +
124A ILE* 4.1 3.4 - - + -
144A LEU 3.6 0.3 - - - +
145A LYS* 3.3 9.3 - - - +
146A ALA 2.8 36.4 + - - +
148A ILE* 3.7 25.4 - - - -
187A VAL* 3.8 18.2 - - + -
188A VAL 3.2 6.7 - - - +
189A CYS* 2.0 46.2 - - - -
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Residues in contact with LEU 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A TYR* 3.7 22.7 - - - +
17A THR* 5.8 3.1 - - + +
18A VAL* 4.4 20.0 - - + -
20A TYR* 4.0 20.7 + - - +
122A CYS* 1.3 73.1 - - - +
124A ILE* 1.3 64.6 + - - +
125A SER* 4.2 2.4 + - - -
143A CYS* 4.0 17.7 - - + -
144A LEU 3.5 15.0 - - - +
145A LYS* 4.4 7.9 - - + -
186A PRO* 3.6 3.1 - - - +
187A VAL* 3.5 2.4 - - - -
188A VAL* 2.8 36.9 + - + +
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Residues in contact with ILE 124 (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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7A ILE* 4.1 7.7 - - + +
122A CYS* 4.8 1.3 - - + +
123A LEU* 1.3 77.9 - - - +
125A SER* 1.3 65.3 + - - +
142A LYS 4.1 0.2 - - - +
143A CYS* 3.5 1.2 - - - -
144A LEU* 2.8 51.3 + - + +
146A ALA* 4.1 25.1 - - + +
169A ALA* 4.6 7.6 - - + -
178A SER* 4.1 23.1 - - - -
186A PRO 3.5 11.0 - - - +
187A VAL* 4.0 17.0 - - + -
197A VAL* 4.1 13.7 - - + -
212A TYR* 3.3 30.5 - - + +
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Residues in contact with SER 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ILE* 4.1 7.9 - - - +
13A CYS* 4.5 0.2 - - - -
18A VAL* 3.7 13.8 - - - +
20A TYR* 4.9 0.9 + - - -
21A GLN* 2.7 33.2 + - - +
123A LEU* 5.0 3.2 + - - +
124A ILE* 1.3 79.5 - - - +
126A GLY* 1.3 59.2 + - - +
141A LEU* 4.4 6.5 - - - -
142A LYS 3.2 13.0 - - - -
143A CYS* 4.1 14.4 - - - -
182A ASP* 4.4 5.4 - - - +
185A GLY* 4.5 5.5 - - - -
186A PRO* 3.5 22.9 + - - +
197A VAL* 4.9 0.7 - - - +
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Residues in contact with GLY 126 (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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7A ILE* 3.8 2.5 + - - +
21A GLN* 4.1 7.2 - - - -
125A SER* 1.3 77.3 - - - +
127A TRP* 1.3 58.4 + - - -
128A GLY 3.7 0.9 + - - -
141A LEU* 3.5 14.8 - - - +
142A LYS* 3.1 36.0 + - - +
182A ASP* 3.1 21.0 - - - +
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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