Contacts of the strand formed by residues 110 - 117 (chain B) in PDB entry 6IEH
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 110 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B THR* 2.5 39.7 + - - +
107B VAL 5.3 0.2 - - - +
108B GLU 3.9 12.3 - - - +
109B GLY* 1.3 77.2 + - - +
111B THR* 1.3 67.2 + - - +
112B HIS* 5.7 0.2 - - - -
142B ALA* 4.4 8.3 - - + -
143B PHE* 3.8 34.5 - - + +
146B GLU* 4.4 8.3 - - - -
307B ILE* 4.9 4.0 - - - -
308B TYR 3.6 8.1 - - - -
309B THR* 4.1 9.2 - - - +
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Residues in contact with THR 111 (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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104B VAL 5.4 0.4 - - - +
106B THR* 4.0 0.2 - - - -
109B GLY 5.4 0.5 - - - -
110B CYS* 1.3 78.4 + - - +
112B HIS* 1.3 62.2 + - - +
113B GLU* 4.0 25.6 - - + +
306B VAL 4.5 0.7 - - - +
307B ILE* 3.4 5.5 - - - +
308B TYR* 2.9 49.5 + - + +
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Residues in contact with HIS 112 (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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103B SER* 4.0 0.5 - - - -
104B VAL* 2.7 72.8 + - + +
106B THR* 3.7 12.9 + - + -
110B CYS* 5.7 0.2 - - - -
111B THR* 1.3 75.8 - - - +
113B GLU* 1.3 69.4 + - - +
125B LEU* 4.2 23.1 - - + -
146B GLU* 3.2 25.0 + - + +
149B GLN* 5.3 1.1 - - - -
150B CYS* 4.3 4.9 - - - -
305B HIS* 3.5 20.4 + - - -
306B VAL 3.7 3.1 - - - -
307B ILE* 3.7 25.7 - - + +
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Residues in contact with GLU 113 (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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101B VAL* 4.3 7.6 - - + -
102B GLN 3.4 11.4 - - - +
103B SER* 4.5 14.9 - - - -
104B VAL* 4.1 0.4 - - - -
111B THR* 4.0 20.2 - - + +
112B HIS* 1.3 83.4 - - - +
114B VAL* 1.3 61.6 + - - +
290B ARG* 3.0 49.0 + - - +
305B HIS* 3.5 2.6 - - - -
306B VAL* 3.0 43.3 + - + +
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Residues in contact with VAL 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B VAL* 3.6 3.9 - - - -
102B GLN* 3.0 31.4 + - + +
104B VAL* 4.4 4.4 - - + +
112B HIS* 4.8 2.0 - - - +
113B GLU* 1.3 74.7 - - - +
115B ALA* 1.3 71.3 + - - +
116B LEU* 3.7 15.3 + - + +
122B TYR* 3.7 36.8 - - + -
303B PRO* 4.2 5.4 - - + -
304B CYS 3.8 4.5 - - - +
305B HIS* 3.0 42.0 - - + +
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Residues in contact with ALA 115 (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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99B VAL* 4.3 3.8 - - + -
100B LYS 3.5 8.5 - - - +
101B VAL* 4.3 6.5 - - + +
113B GLU 4.3 0.2 - - - -
114B VAL* 1.3 73.7 - - - +
116B LEU* 1.3 59.4 + - - +
290B ARG* 5.4 0.9 - - + +
293B ALA* 3.9 27.1 - - + +
294B GLU* 4.1 22.0 - - + +
297B CYS* 4.0 4.7 - - + +
303B PRO* 3.4 3.8 - - - +
304B CYS 3.1 30.5 + - - +
306B VAL* 5.7 1.7 - - + +
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Residues in contact with LEU 116 (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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99B VAL* 3.7 2.9 - - - +
100B LYS* 3.0 55.5 + - + +
102B GLN* 4.6 5.6 - - + -
114B VAL* 4.1 28.0 - - + +
115B ALA* 1.3 77.0 - - - +
117B PRO* 1.3 79.3 - - + +
120B GLU* 4.7 4.0 - - + +
121B ASP 4.9 3.6 - - - +
122B TYR* 3.9 41.1 - - + +
123B LEU 5.2 1.6 - - - +
155B GLN* 5.6 1.8 - - - +
297B CYS* 3.4 6.1 - - - -
303B PRO* 4.2 15.7 - - + -
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Residues in contact with PRO 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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98B ARG 4.2 5.2 - - - +
99B VAL* 4.7 0.4 - - + -
100B LYS* 4.1 0.3 - - - -
116B LEU* 1.3 91.3 - - + +
118B ALA* 1.3 63.8 + - - +
119B GLU* 3.1 21.0 + - + +
120B GLU* 3.1 28.1 + - + +
297B CYS* 3.3 13.2 - - - -
301B LYS* 3.9 13.0 - - + +
302B GLN* 3.8 33.0 - - - +
303B PRO* 4.3 5.2 - - + -
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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