Contacts of the strand formed by residues 122 - 129 (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 LEU 122 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A GLY* 1.3 79.1 - - - +
123A SER* 1.3 68.0 + - - +
124A VAL* 3.4 7.0 + - + +
138A THR* 6.0 8.1 - - + -
174A GLU* 3.3 6.4 + - - -
175A VAL* 2.9 36.5 + - + +
201A ARG* 2.7 43.7 - - + +
202A ASN* 6.2 0.4 - - - +
204A ALA* 3.5 17.7 - - + -
205A ALA* 3.3 30.7 - - + +
208A LEU* 5.7 5.8 - - + -
209A ARG* 4.9 8.7 - - - +
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Residues in contact with SER 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A MET* 4.5 8.5 - - - -
122A LEU* 1.3 76.1 - - - +
124A VAL* 1.3 63.0 + - - +
138A THR* 3.8 3.5 - - - -
139A ARG* 3.1 50.7 + - - +
173A GLY 3.5 10.8 - - - -
174A GLU* 3.2 15.5 + - - +
201A ARG* 4.2 11.1 + - - +
226A TYR* 4.5 6.4 + - - -
700A AMP 4.4 7.6 + - - -
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Residues in contact with VAL 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A MET* 3.6 10.1 - - - +
122A LEU* 3.4 15.7 - - + +
123A SER* 1.3 76.5 - - - +
125A ASN* 1.3 59.0 + - - +
126A LEU* 4.2 12.3 + - + -
137A ALA 3.4 9.6 - - - +
138A THR* 4.9 3.8 - - + -
148A VAL* 6.0 0.2 - - + -
152A LEU* 4.7 7.9 - - + -
158A ILE* 6.1 0.2 - - + -
171A VAL 4.4 0.2 - - - +
172A ARG* 3.8 2.3 - - - -
173A GLY 3.2 25.8 + - - +
174A GLU* 4.3 4.9 - - - -
175A VAL* 3.9 23.6 - - + -
208A LEU* 4.5 15.0 - - + -
225A PHE* 3.5 32.1 - - + -
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Residues in contact with ASN 125 (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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78A HIS* 3.1 36.6 + - + +
79A PRO* 5.4 2.0 - - - -
82A MET* 3.4 20.7 - - - +
124A VAL* 1.3 74.8 - - - +
126A LEU* 1.3 73.1 + - - +
127A TYR* 4.1 2.7 + - - +
135A PHE* 6.1 3.8 - - + -
136A GLY* 2.9 5.0 - - - -
137A ALA* 2.6 41.3 + - + +
170A GLU* 3.0 44.6 + - - +
171A VAL 3.9 4.8 - - - +
172A ARG* 3.7 7.5 + - - +
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Residues in contact with LEU 126 (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* 4.2 16.2 - - + -
125A ASN* 1.3 85.2 + - - +
127A TYR* 1.3 60.3 + - - +
128A TYR* 3.0 46.0 - - + +
133A LEU* 4.1 9.6 - - + -
135A PHE 3.7 2.9 - - - -
136A GLY* 4.0 0.7 - - - -
152A LEU* 3.1 34.8 - - + -
158A ILE* 3.3 25.4 - - + -
169A LEU 3.6 0.2 - - - +
171A VAL* 3.2 34.5 + - + +
225A PHE* 3.7 17.3 - - + -
252A PHE* 4.5 0.9 - - + -
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Residues in contact with TYR 127 (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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79A PRO* 4.1 19.5 - - + -
125A ASN* 4.1 3.3 + - - +
126A LEU* 1.3 69.1 - - - +
128A TYR* 1.3 80.9 + - - +
129A GLU* 2.9 44.0 + - + +
133A LEU* 3.5 1.0 - - - +
134A VAL* 3.1 40.8 + - + -
135A PHE* 3.1 48.6 + + + +
168A ARG* 2.9 50.0 + - + -
169A LEU 3.5 11.9 - - - -
170A GLU* 4.5 5.6 - - + +
230A LEU* 5.6 1.6 - - + -
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Residues in contact with TYR 128 (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* 3.0 63.8 - - + +
127A TYR* 1.3 79.1 - - - +
129A GLU* 1.3 62.6 + - - +
131A GLY* 3.0 26.9 + - - +
132A VAL 3.2 4.5 - - - +
133A LEU* 3.6 26.1 - - + +
134A VAL 4.3 0.2 - - - +
158A ILE* 4.0 0.3 - - - +
159A PRO 3.0 22.5 + - - -
160A ARG 4.1 1.6 - - - -
162A LEU* 3.1 29.6 - - + -
166A PRO 4.8 0.2 - - - +
167A ASP 3.7 0.9 - - - +
168A ARG* 3.6 3.8 - - - -
169A LEU* 2.7 50.8 + - + +
171A VAL* 4.2 2.9 - - + -
252A PHE* 3.4 19.9 - + - -
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Residues in contact with GLU 129 (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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7A ARG* 2.5 44.5 + - - +
11A ASN* 3.2 14.3 + - - +
127A TYR* 2.9 44.4 + - + +
128A TYR* 1.3 71.2 - - - +
130A GLU* 1.3 65.6 + - - +
131A GLY 2.5 17.1 + - - -
132A VAL* 2.6 28.3 + - - +
134A VAL* 3.8 20.2 - - + +
167A ASP 3.3 5.4 - - - +
168A ARG* 5.0 3.1 - - + -
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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