Contacts of the strand formed by residues 109 - 115 (chain B) in PDB entry 2I6A
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 ASP 109 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7B ASN* 3.0 30.2 + - - +
82B LYS* 3.6 41.6 - - + +
84B ALA 3.0 17.0 + - - +
85B THR* 3.5 1.6 - - - -
86B PHE 3.2 20.0 + - - -
107B HIS 3.7 2.6 + - - -
108B VAL* 1.3 66.8 - - - +
110B ALA* 1.3 60.8 + - - +
111B HIS* 2.9 39.4 + - - -
158B LEU* 4.0 4.5 - - - +
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Residues in contact with ALA 110 (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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86B PHE* 3.4 11.4 - - + +
103B ALA* 3.8 17.9 - - + -
108B VAL* 3.0 14.6 + - + +
109B ASP* 1.3 73.9 + - - +
111B HIS* 1.3 70.1 + - - +
112B TYR* 3.5 37.2 + - + +
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Residues in contact with HIS 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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85B THR* 4.3 0.2 - - + -
86B PHE 2.9 10.7 + - - -
87B PHE* 3.4 32.0 - + + -
88B GLY 3.7 0.2 + - - -
109B ASP* 2.9 39.6 + - - -
110B ALA* 1.3 76.2 + - - +
112B TYR* 1.3 61.9 + - - +
149B HIS* 3.2 23.2 + - + +
155B ASN* 4.6 10.0 + - - +
158B LEU* 3.0 35.1 - - + +
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Residues in contact with TYR 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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15B PRO* 3.9 10.1 - - + -
67B GLN* 2.6 29.5 + - - -
86B PHE* 3.8 15.3 - + - -
88B GLY 3.0 23.6 - - - +
90B ILE* 3.6 32.5 - - + -
99B LEU* 3.6 8.9 + - + -
100B LYS* 3.7 35.2 - - + -
103B ALA* 3.4 18.4 - - - +
110B ALA* 3.5 24.9 - - + +
111B HIS* 1.3 78.2 - - - +
113B TYR* 1.3 61.2 + - - +
114B GLU* 3.8 12.0 + - + +
149B HIS* 3.9 7.2 + - - -
92D ILE* 6.0 1.4 - - - +
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Residues in contact with TYR 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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88B GLY 2.7 13.3 + - - +
89B CYS* 3.4 29.7 - - + -
90B ILE* 3.0 27.4 + - - +
112B TYR* 1.3 73.3 - - - +
114B GLU* 1.3 62.8 + - - +
115B GLN* 4.0 20.2 - - + +
143B CYS* 4.2 11.4 - - + -
144B TYR* 4.7 4.9 - + + -
145B LYS 6.1 0.9 - - - -
148B LYS* 3.4 60.8 + - + -
149B HIS* 3.8 24.2 - + + -
116D ASN* 3.5 34.2 + - + +
117D GLU* 4.7 7.1 + - - -
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Residues in contact with GLU 114 (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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90B ILE* 3.7 24.6 - - + +
91B GLY 5.0 3.4 - - - +
92B ILE* 4.0 21.8 - - + +
100B LYS* 3.1 36.4 + - - +
112B TYR* 3.8 11.4 + - + +
113B TYR* 1.3 80.1 - - - +
115B GLN* 1.3 61.9 + - - +
92D ILE* 4.1 30.8 - - + +
116D ASN* 2.7 36.0 + - - +
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Residues in contact with GLN 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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89B CYS* 3.8 18.2 - - - -
90B ILE 2.7 26.6 + - - +
91B GLY* 3.3 1.2 - - - -
92B ILE* 2.8 34.1 + - - +
113B TYR* 4.0 13.2 - - + +
114B GLU* 1.3 78.3 - - - +
116B ASN* 1.3 64.2 + - - +
117B GLU* 3.4 21.3 + - - +
118B GLN* 2.5 55.7 - - - +
140B ALA* 3.6 2.6 - - - +
143B CYS* 3.9 15.3 - - + +
92D ILE* 5.6 0.4 - - - -
116D ASN* 4.9 2.0 - - - +
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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