Contacts of the strand formed by residues 168 - 176 (chain A) in PDB entry 1V9P
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 168 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A PRO* 4.3 18.0 - - - +
127A TYR* 2.9 42.0 + - + +
128A TYR 3.6 4.3 - - - -
129A GLU* 5.0 3.4 - - + -
130A GLU* 5.7 1.3 - - - +
166A PRO* 2.9 15.3 - - - +
167A ASP* 1.3 86.7 - - + +
169A LEU* 1.3 60.1 + - - +
230A LEU* 3.0 38.7 - - + +
231A GLY* 3.9 0.3 - - - -
234A GLU* 5.1 2.3 + - - +
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Residues in contact with LEU 169 (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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126A LEU 3.6 1.6 - - - +
127A TYR* 3.5 5.3 - - - -
128A TYR* 2.7 48.3 + - + +
162A LEU* 3.3 31.4 - - + -
165A VAL* 3.8 21.3 - - + -
166A PRO* 4.0 15.5 - - + +
168A ARG* 1.3 74.7 - - - +
170A GLU* 1.3 68.7 + - - +
171A VAL* 3.3 25.6 - - + -
228A LEU* 4.2 19.3 - - + -
230A LEU 3.0 8.7 - - - +
231A GLY* 4.1 11.4 - - - -
246A TRP* 4.0 9.0 - - + -
252A PHE* 4.7 0.2 - - + -
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Residues in contact with GLU 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A PRO* 3.1 17.8 - - + +
80A THR* 2.7 41.9 + - - +
125A ASN* 3.0 40.3 + - - +
126A LEU 3.8 3.8 - - - +
127A TYR* 4.5 7.0 - - + +
169A LEU* 1.3 77.2 - - - +
171A VAL* 1.3 58.4 + - - +
172A ARG* 3.2 9.8 + - - +
228A LEU 3.3 1.4 - - - -
229A GLY 2.6 30.0 + - - -
230A LEU* 2.8 42.4 + - + +
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Residues in contact with VAL 171 (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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124A VAL 4.4 0.3 - - - +
125A ASN* 3.9 0.7 - - - +
126A LEU* 3.2 44.1 + - + +
128A TYR* 4.8 1.3 - - + -
169A LEU* 3.3 33.0 - - + -
170A GLU* 1.3 72.6 - - - +
172A ARG* 1.3 59.4 + - - +
173A GLY 4.5 0.2 + - - -
225A PHE* 4.4 11.9 - - + -
227A ALA 3.4 8.5 - - - +
228A LEU* 4.1 9.6 - - + -
246A TRP* 5.4 0.2 - - + -
247A LEU* 4.5 6.3 - - + -
252A PHE* 3.4 46.7 - - + -
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Residues in contact with ARG 172 (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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80A THR* 2.5 31.6 + - - -
81A ARG 3.0 20.4 + - - -
82A MET* 3.1 52.0 - - + +
83A TYR 5.1 0.4 - - - +
124A VAL 3.8 3.4 - - - -
125A ASN* 3.7 5.1 - - - +
170A GLU* 3.2 39.8 + - - +
171A VAL* 1.3 74.4 - - - +
173A GLY* 1.3 58.7 + - - +
225A PHE* 3.5 6.7 - - - +
226A TYR* 3.1 11.0 + - + +
227A ALA* 2.7 47.8 + - + +
228A LEU 3.8 13.7 + - - -
229A GLY* 3.7 6.3 - - - -
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Residues in contact with GLY 173 (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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82A MET* 5.5 0.2 - - - +
123A SER* 3.5 1.6 - - - -
124A VAL* 3.2 20.2 + - - +
172A ARG* 1.3 76.1 - - - +
174A GLU* 1.3 71.0 + - - +
224A THR 3.2 5.2 - - - -
225A PHE* 3.1 23.1 - - - -
226A TYR* 3.4 20.2 + - - -
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Residues in contact with GLU 174 (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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119A VAL* 2.8 38.4 - - + +
121A GLY* 2.9 31.2 + - - +
122A LEU 3.3 9.6 - - - +
123A SER* 3.2 23.1 + - - -
124A VAL* 4.3 4.8 - - - +
173A GLY* 1.3 81.8 - - - +
175A VAL* 1.3 62.2 + - - +
176A TYR* 4.2 1.5 - - - -
201A ARG* 3.9 2.3 + - - -
223A ALA* 3.1 6.1 - - - +
224A THR* 2.6 38.9 + - + +
225A PHE* 4.2 1.2 - - - -
226A TYR* 3.8 17.4 - - + +
700A AMP 3.4 19.9 - - + +
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Residues in contact with VAL 175 (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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121A GLY* 3.8 0.3 - - - -
122A LEU* 2.9 30.7 + - + +
124A VAL* 3.9 25.6 - - + -
152A LEU* 4.6 11.2 - - + -
155A ILE* 3.6 13.7 - - + -
158A ILE* 4.6 2.7 - - + -
174A GLU* 1.3 73.0 - - - +
176A TYR* 1.3 63.7 + - - +
204A ALA* 3.9 9.5 - - + +
208A LEU* 4.4 14.1 - - + -
221A LEU* 3.9 30.7 - - + -
222A ARG 3.3 3.4 - - - +
223A ALA* 3.3 24.5 - - + -
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Residues in contact with TYR 176 (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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119A VAL* 3.9 21.3 - - + -
120A ASP 4.0 20.0 - - - +
121A GLY* 4.1 4.9 - - - -
174A GLU 4.6 2.0 - - - -
175A VAL* 1.3 77.2 - - - +
177A MET* 1.3 66.2 + - - +
178A PRO* 3.8 17.2 - - + +
204A ALA* 4.0 9.4 - - - -
221A LEU* 3.3 4.4 - - - -
222A ARG* 2.5 79.0 + - + +
223A ALA* 4.0 9.2 - - - -
224A THR* 4.4 6.7 - - + -
255A GLU* 2.7 30.7 + - + +
256A HIS 6.3 0.2 - - - -
282A PRO* 5.4 2.8 - - - +
283A PHE* 3.6 42.8 - + + -
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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