Contacts of the strand formed by residues 154 - 167 (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 ARG 154 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A ILE* 4.0 2.1 - - - +
141A GLN* 3.2 49.0 + - + +
142A ARG* 3.4 41.3 + - + +
153A LEU* 1.3 73.4 + - - +
155A THR* 1.3 64.6 + - - +
156A ARG* 3.3 35.1 - - - +
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Residues in contact with THR 155 (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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138A GLU* 3.1 25.6 + - + -
139A ILE 3.3 18.2 - - - +
140A ILE* 4.5 2.5 - - - -
141A GLN* 4.4 2.7 - - - +
153A LEU* 3.9 29.7 + - + +
154A ARG* 1.3 82.0 + - - +
156A ARG* 1.3 85.1 + - - +
178A GLU* 4.5 1.0 - - - +
48B VAL* 4.5 14.6 - - + -
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Residues in contact with ARG 156 (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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138A GLU* 3.8 5.1 - - - -
139A ILE* 2.9 42.5 + - + +
141A GLN* 3.2 43.4 - - + +
154A ARG* 3.3 29.8 - - - +
155A THR* 1.3 90.9 + - - +
157A LYS* 1.3 60.4 + - - +
178A GLU* 3.6 25.2 + - + +
179A ALA 3.6 20.9 + - - -
180A GLY* 3.7 11.5 + - - -
181A THR* 2.8 33.9 - - + +
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Residues in contact with LYS 157 (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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137A GLY 3.5 4.5 - - - +
138A GLU* 3.1 45.5 + - + +
156A ARG* 1.3 73.0 - - - +
158A VAL* 1.3 61.5 + - - +
159A TYR* 3.9 30.2 + - + +
177A VAL* 3.5 4.0 - - - +
178A GLU* 2.8 57.7 + - + +
181A THR* 4.1 1.4 + - - -
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Residues in contact with VAL 158 (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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135A PHE 3.2 27.4 - - - +
136A GLU* 3.6 3.3 - - - -
137A GLY* 2.7 39.1 + - - +
139A ILE* 3.7 24.7 - - + -
156A ARG 3.8 0.2 + - - -
157A LYS* 1.3 73.3 - - - +
159A TYR* 1.3 64.4 + - - +
160A TYR 3.8 11.0 - - - +
161A ILE* 3.8 27.4 - - + -
175A VAL* 4.0 4.0 - - + -
176A GLY 3.7 5.8 - - - +
177A VAL* 3.9 14.1 - - + -
181A THR* 4.7 4.5 - - + -
186A LEU* 4.7 8.7 - - + -
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Residues in contact with TYR 159 (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* 4.9 2.8 + - - -
12A ILE 4.0 9.1 - - - +
13A LEU* 3.9 14.8 - - + -
14A PRO* 3.5 39.4 - - + +
110A GLY* 5.0 3.4 - - - -
136A GLU* 4.7 5.7 - - - +
157A LYS* 4.0 29.8 - - + +
158A VAL* 1.3 75.9 - - - +
160A TYR* 1.3 76.0 + - + +
176A GLY 2.8 13.4 + - - +
177A VAL 3.6 15.7 - - - -
178A GLU* 3.5 37.0 - - - +
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Residues in contact with TYR 160 (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* 3.3 55.7 + - + +
12A ILE* 3.6 18.6 - - + -
13A LEU* 3.4 30.8 + - + +
112A GLU* 2.6 35.2 + - + +
136A GLU* 3.4 11.7 - - - +
158A VAL* 3.4 1.4 - - - +
159A TYR* 1.3 88.3 - - + +
161A ILE* 1.3 66.5 + - - +
162A GLU* 5.0 7.2 - - + -
174A ARG* 4.6 9.0 - - - -
175A VAL* 3.4 12.7 - - - +
176A GLY* 3.1 41.5 + - - -
207A ARG* 5.4 4.0 + - - -
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Residues in contact with ILE 161 (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* 3.8 10.4 + - - -
132A MET* 3.3 47.3 - - + +
133A LYS* 5.7 1.5 - - - -
135A PHE* 3.9 21.3 - - + +
136A GLU* 2.7 21.9 + - + +
158A VAL* 3.8 17.7 - - + -
160A TYR* 1.3 79.0 - - - +
162A GLU* 1.3 61.1 + - - +
163A VAL* 4.1 4.6 + - + +
173A PHE* 3.8 24.5 - - + -
174A ARG 3.4 3.1 - - - -
175A VAL* 3.8 12.8 - - + -
186A LEU* 4.8 10.8 - - + -
190A ILE* 4.9 4.9 - - + -
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Residues in contact with GLU 162 (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* 5.2 17.3 + - + +
160A TYR* 4.2 6.8 - - + -
161A ILE* 1.3 72.5 - - - +
163A VAL* 1.3 67.1 + - - +
164A LEU* 3.3 28.5 + - + +
173A PHE* 4.0 2.5 - - - -
174A ARG* 2.8 58.5 + - + +
13C ARG* 4.6 7.3 + - - -
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Residues in contact with VAL 163 (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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128A ILE* 5.2 0.7 - - + -
129A ILE* 4.6 25.8 - - + +
132A MET* 3.9 35.9 - - + -
161A ILE* 4.0 6.8 + - + +
162A GLU* 1.3 74.7 - - - +
164A LEU* 1.3 63.9 + - - +
165A GLU* 4.2 5.6 - - - +
166A ILE* 4.0 33.0 - - + -
171A VAL* 4.2 4.3 - - + -
172A LEU 3.9 9.4 - - - +
173A PHE* 3.9 2.5 - - + -
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Residues in contact with LEU 164 (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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114A VAL* 4.5 4.5 - - + -
162A GLU* 3.7 40.6 - - + +
163A VAL* 1.3 74.8 - - - +
165A GLU* 1.3 62.5 + - + +
172A LEU* 2.8 29.6 + - + +
173A PHE 4.3 1.3 - - - -
174A ARG* 4.1 26.2 - - + +
13C ARG* 3.0 42.8 + - - +
14C TYR* 3.8 39.3 - - + +
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Residues in contact with GLU 165 (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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163A VAL* 3.7 2.4 - - - -
164A LEU* 1.3 82.7 - - + +
166A ILE* 1.3 66.4 + - - +
167A GLU* 4.1 0.8 + - + +
170A ASP 4.0 0.2 - - - +
171A VAL* 3.8 1.7 - - - +
172A LEU* 3.0 44.0 + - + +
13C ARG* 5.2 1.7 + - - -
14C TYR 4.4 1.6 - - - +
15C THR* 2.7 29.7 + - - -
16C LEU* 2.7 39.4 + - + +
17C LYS* 3.6 23.7 + - - +
21C PRO* 4.4 9.9 - - - +
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Residues in contact with ILE 166 (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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123A VAL 5.8 0.2 - - - +
125A GLU* 3.7 52.9 + - + +
128A ILE* 4.0 35.4 - - + -
129A ILE* 4.5 6.5 - - + -
163A VAL* 4.0 17.9 - - + -
165A GLU* 1.3 79.4 - - - +
167A GLU* 1.3 62.5 + - - +
168A GLY 3.7 22.5 + - - +
170A ASP 3.4 6.1 - - - +
171A VAL* 3.9 14.8 - - + -
17C LYS* 5.2 3.2 + - - -
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Residues in contact with GLU 167 (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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165A GLU* 4.1 1.0 - - - +
166A ILE* 1.3 71.4 - - - +
168A GLY* 1.3 62.0 + - - +
169A ARG 3.3 0.9 + - - -
170A ASP* 2.9 27.3 + - - +
501A ATP 5.6 0.7 + - - -
4C ARG* 2.8 31.0 + - - -
16C LEU* 4.0 29.7 - - + +
17C LYS* 3.7 36.9 + - - +
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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