Contacts of the strand formed by residues 111 - 117 (chain A) in PDB entry 6C90
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 THR 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A THR* 4.7 0.4 - - - -
110A CYS* 1.3 76.1 + - - +
112A HIS* 1.3 65.3 + - - +
113A GLU* 4.2 21.5 - - + +
306A VAL 3.3 4.0 - - - +
307A ILE* 3.4 5.4 - - - +
308A TYR* 2.7 51.6 + - + +
1108A TLA 4.3 15.1 + - - +
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Residues in contact with HIS 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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103A SER* 4.8 0.3 - - - -
104A VAL* 2.9 54.3 + - + +
106A THR* 3.6 21.4 + - + -
110A CYS 4.3 0.4 + - - -
111A THR* 1.3 76.6 - - - +
113A GLU* 1.3 82.9 + - - +
125A LEU* 4.2 17.7 - - + -
146A GLU* 2.9 35.0 + - + +
150A CYS* 4.3 2.2 - - - -
305A HIS* 3.0 31.4 + + + +
306A VAL 3.3 2.5 - - - -
307A ILE* 3.5 17.2 - - + +
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Residues in contact with GLU 113 (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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101A VAL* 4.0 12.1 - - + +
102A GLN 3.4 11.4 - - - +
103A SER* 3.8 17.3 + - - +
104A VAL 4.6 0.2 - - - +
111A THR* 4.2 14.1 - - + +
112A HIS* 1.3 89.6 - - - +
114A VAL* 1.3 59.4 + - - +
290A ARG* 2.9 45.8 + - - +
305A HIS* 3.3 1.0 - - - -
306A VAL* 2.7 42.7 + - + +
1108A TLA 2.9 25.8 - - - +
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Residues in contact with VAL 114 (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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101A VAL* 3.4 4.3 - - - -
102A GLN* 2.8 50.3 + - + +
104A VAL* 4.3 5.8 - - + -
112A HIS* 4.8 0.2 - - - +
113A GLU* 1.3 77.5 - - - +
115A ALA* 1.3 74.4 + - - +
116A LEU* 3.5 6.3 - - + +
122A TYR* 3.8 23.6 - - + -
303A PRO* 3.8 15.5 - - + -
304A CYS 3.6 8.7 - - - +
305A HIS* 3.5 31.4 - - + +
306A VAL* 6.0 0.2 - - - -
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Residues in contact with ALA 115 (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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99A VAL* 3.9 9.6 - - + -
100A LYS 3.3 6.1 - - - +
101A VAL* 4.3 5.3 - - + +
114A VAL* 1.3 74.1 - - - +
116A LEU* 1.3 59.0 + - - +
290A ARG* 5.2 0.4 - - + +
293A ALA* 3.8 27.9 - - + +
294A GLU* 3.8 25.6 - - + +
297A CYS* 3.8 4.4 - - + -
303A PRO* 3.1 4.3 - - - +
304A CYS 2.9 33.7 + - - +
306A VAL* 5.6 0.8 - - - +
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Residues in contact with LEU 116 (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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99A VAL* 3.6 3.3 - - - -
100A LYS* 2.9 62.9 + - + +
102A GLN* 4.0 19.3 - - + -
114A VAL* 3.5 24.0 - - + +
115A ALA* 1.3 74.7 - - - +
117A PRO* 1.3 79.8 - - + +
120A GLU* 3.9 10.3 - - + +
121A ASP 4.0 4.0 - - - +
122A TYR* 3.7 31.9 - - + +
297A CYS* 3.2 6.5 - - - -
303A PRO* 4.3 14.1 - - + -
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Residues in contact with PRO 117 (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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98A ARG 3.7 7.6 - - - +
100A LYS* 3.8 3.5 - - - -
116A LEU* 1.3 89.5 - - + +
118A ALA* 1.3 67.0 + - - +
119A GLU* 3.4 25.1 - - - +
120A GLU* 3.1 51.1 + - - +
297A CYS* 3.3 12.3 - - - +
301A LYS* 3.9 27.4 - - + +
302A GLN 4.2 9.6 - - - -
303A PRO* 4.4 1.1 - - + -
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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