Contacts of the strand formed by residues 111 - 119 (chain A) in PDB entry 2HVY
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 LYS 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A LEU* 4.2 4.5 - - - +
82A GLY* 4.6 7.6 - - - -
106A LEU 3.2 19.5 + - - -
107A LEU* 3.4 13.3 + - - +
109A ALA 2.7 25.6 + - - +
110A GLY* 1.3 76.6 - - - +
112A GLU* 1.3 61.1 + - - +
113A TYR* 3.7 28.7 - - + +
176A GLY* 3.4 2.6 - - - -
177A VAL* 2.8 39.1 + - + +
178A GLU 5.4 0.2 - - - +
179A ALA* 4.1 11.4 - - - +
205A ARG* 3.6 27.4 - - - +
207A ARG 3.5 4.7 - - - +
208A SER* 3.7 25.4 - - - +
209A GLY 4.6 0.2 - - - +
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Residues in contact with GLU 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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11A ARG 4.5 2.9 + - - -
13A LEU* 5.0 0.7 - - + -
111A LYS* 1.3 74.9 - - - +
113A TYR* 1.3 66.9 + - - +
160A TYR* 2.6 32.3 + - - +
174A ARG* 3.0 40.7 + - + -
175A VAL 3.3 10.5 - - - +
205A ARG* 3.4 10.2 - - - +
206A THR* 2.7 43.0 + - - +
207A ARG* 3.1 35.7 + - + +
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Residues in contact with TYR 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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84A LEU* 4.4 9.6 - - + +
111A LYS* 3.7 27.1 - - + +
112A GLU* 1.3 75.6 - - - +
114A VAL* 1.3 62.9 - - - +
115A ALA 4.1 0.2 - - - -
174A ARG* 3.3 7.1 - - - +
175A VAL* 2.9 43.9 + - + +
177A VAL* 3.9 14.8 - - + -
181A THR 4.8 6.4 + - - -
183A ILE* 3.6 28.7 - - + -
203A LEU* 3.7 39.5 - - + -
204A ARG 3.3 4.7 - - - +
205A ARG* 3.7 44.9 + - + -
206A THR* 4.0 3.6 - - - -
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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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113A TYR* 1.3 76.3 - - - +
115A ALA* 1.3 62.5 + - - +
164A LEU* 4.5 2.5 - - + -
172A LEU* 3.8 26.5 - - + -
173A PHE 3.4 7.2 - - - +
174A ARG* 4.0 19.5 - - + -
203A LEU* 3.8 2.1 - - - +
204A ARG* 2.8 38.3 + - + +
206A THR* 3.6 16.1 - - + +
5C ILE* 4.1 9.1 - - + +
14C TYR* 3.6 47.6 - - + -
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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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113A TYR 4.1 0.2 - - - -
114A VAL* 1.3 74.3 - - - +
116A LEU* 1.3 60.5 + - - +
117A MET 4.0 0.2 - - - -
172A LEU* 3.5 8.4 - - - +
173A PHE* 2.9 60.7 + - + +
175A VAL* 5.1 2.2 - - + -
183A ILE* 4.1 9.4 - - + -
187A ILE* 4.1 5.4 - - + -
202A GLU 3.5 7.0 - - - +
203A LEU* 3.6 20.6 - - + -
5C ILE* 4.4 0.7 - - - -
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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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115A ALA* 1.3 72.5 - - - +
117A MET* 1.3 59.0 + - - +
170A ASP* 3.9 22.2 - - + +
171A VAL 3.6 23.6 - - - +
172A LEU* 3.9 5.6 - - + +
187A ILE* 4.6 2.5 - - - -
200A MET* 3.6 4.7 - - - +
201A SER* 3.0 45.6 + - - +
202A GLU* 2.9 26.9 + - + +
4C ARG* 3.6 41.7 - - + +
5C ILE* 4.1 8.5 - - + +
16C LEU* 3.9 22.9 - - + -
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Residues in contact with MET 117 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A ALA 4.0 0.6 - - - -
116A LEU* 1.3 73.2 - - - +
118A HIS* 1.3 60.7 - - - +
119A LEU* 4.0 14.1 - - + -
128A ILE* 4.7 3.4 - - + -
132A MET* 3.7 31.9 - - + -
169A ARG 3.4 2.4 - - - +
170A ASP* 3.4 3.7 - - - -
171A VAL* 2.8 61.4 + - + +
173A PHE* 4.0 10.1 - - + -
187A ILE* 3.6 28.9 - - + -
190A ILE* 3.8 28.3 - - + -
194A LEU* 4.7 0.2 - - + -
198A ALA* 3.7 22.9 - - + -
199A HIS 3.5 4.3 - - - -
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Residues in contact with HIS 118 (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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116A LEU 4.0 1.4 + - - -
117A MET* 1.3 72.1 - - - +
119A LEU* 1.3 82.7 + - - +
120A HIS* 3.6 4.7 + + - -
169A ARG* 3.5 10.0 + - + -
170A ASP* 2.7 28.0 + - - +
198A ALA* 3.3 3.4 - - - -
199A HIS* 2.9 49.5 + + + +
201A SER* 4.6 9.0 - - - +
501A ATP 3.1 85.9 + + - -
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Residues in contact with LEU 119 (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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117A MET* 4.0 12.3 - - + -
118A HIS* 1.3 91.2 + - - +
120A HIS* 1.3 57.7 + - - +
121A GLY 3.3 17.3 - - - +
123A VAL* 4.1 16.8 - - + +
128A ILE* 3.7 33.9 - - + -
168A GLY 5.1 0.9 - - - +
169A ARG* 2.8 40.7 + - + +
171A VAL* 4.3 8.3 - - + -
194A LEU* 3.6 25.4 - - + -
196A VAL* 4.2 5.4 - - + -
197A GLY 3.5 6.3 - - - +
198A ALA* 3.8 19.5 - - + -
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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