Contacts of the strand formed by residues 123 - 135 (chain A) in PDB entry 1V8C
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 ALA 123 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119A ARG* 3.6 2.3 - - - +
120A LEU* 2.7 39.0 + - + +
121A PRO 3.4 0.6 - - - -
122A GLY* 1.3 82.1 - - - +
124A VAL* 1.3 64.9 + - - +
125A VAL* 5.3 0.9 - - + -
147A VAL* 4.0 17.9 - - + -
148A GLU 3.2 12.6 - - - +
149A GLY* 4.3 0.9 - - - -
151A GLU 4.2 6.5 - - - +
152A ALA 4.2 0.2 - - - +
155A TRP* 3.7 24.9 - - + -
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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
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113A GLU* 5.1 4.0 - - - +
117A VAL* 3.9 17.5 - - + -
118A TYR 3.4 11.0 - - - +
119A ARG* 3.4 41.5 - - + +
123A ALA* 1.3 76.2 - - - +
125A VAL* 1.3 64.7 + - - +
126A ARG* 3.5 39.2 + - + +
146A GLU 3.7 1.6 - - - +
147A VAL* 3.4 3.5 - - - -
148A GLU* 2.9 37.6 + - + +
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Residues in contact with VAL 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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101A LEU* 4.8 0.9 - - + -
105A LEU* 4.1 16.2 - - + -
116A GLY 3.8 0.9 - - - +
117A VAL* 3.3 4.5 - - - +
118A TYR* 2.8 37.2 + - - +
120A LEU* 3.7 30.7 - - + -
123A ALA 5.3 0.2 - - - -
124A VAL* 1.3 77.6 - - - +
126A ARG* 1.3 64.3 + - - +
127A PHE* 4.2 15.3 - - + -
145A VAL* 4.0 15.9 - - + -
146A GLU 3.4 4.0 - - - +
147A VAL* 4.2 12.8 - - + -
155A TRP* 5.0 0.4 - - + -
159A ILE* 3.8 31.2 - - + -
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Residues in contact with ARG 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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116A GLY 3.2 5.2 - - - +
117A VAL* 4.2 21.6 - - + +
119A ARG* 5.9 1.4 - - - +
124A VAL* 3.5 33.4 + - + +
125A VAL* 1.3 77.2 - - - +
127A PHE* 1.3 63.5 + - - +
144A ARG* 3.9 0.8 + - - +
145A VAL* 3.5 0.9 - - - +
146A GLU* 2.8 62.7 + - + +
148A GLU* 3.6 33.8 + - - +
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Residues in contact with PHE 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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98A PRO* 4.0 26.5 - - + -
101A LEU* 3.6 26.7 - - + -
102A GLU* 3.6 26.7 - - + -
105A LEU* 3.6 22.7 - - + -
115A GLU* 4.9 2.1 - - - +
116A GLY* 2.9 44.2 + - - +
118A TYR* 3.9 12.8 - + - -
125A VAL* 4.2 9.0 - - + -
126A ARG* 1.3 78.1 - - - +
128A ARG* 1.3 64.8 + - - +
143A LEU* 4.2 14.4 - - + -
144A ARG* 3.1 15.0 - - - +
145A VAL* 4.1 6.1 - - + -
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Residues in contact with ARG 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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98A PRO* 6.1 0.4 - - - -
127A PHE* 1.3 77.5 - - - +
129A GLU* 1.3 79.9 + - - +
130A VAL* 3.5 12.0 + - - +
143A LEU* 3.6 6.7 - - - +
144A ARG* 3.0 72.9 + - - +
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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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97A PRO* 5.1 0.9 - - - +
98A PRO* 3.5 40.3 - - + +
128A ARG* 1.3 94.3 + - - +
130A VAL* 1.3 65.1 + - - +
141A PRO* 3.9 23.0 - - - +
142A GLN 3.5 10.4 - - - +
143A LEU* 3.7 5.8 - - + +
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Residues in contact with VAL 130 (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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92A THR* 4.2 13.7 - - + +
128A ARG* 4.0 16.4 - - - +
129A GLU* 1.3 83.7 - - - +
131A GLU* 1.3 65.9 + - - +
132A PRO* 3.3 10.4 - - - +
142A GLN* 2.9 38.9 + - + +
144A ARG* 3.9 31.9 - - + +
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Residues in contact with GLU 131 (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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130A VAL* 1.3 78.2 - - - +
132A PRO* 1.3 89.1 - - - +
133A LEU* 4.6 2.6 - - - +
142A GLN* 3.2 18.4 - - - +
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Residues in contact with PRO 132 (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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130A VAL 3.5 8.3 - - - +
131A GLU* 1.3 113.1 - - - +
133A LEU* 1.3 62.4 + - - +
134A LYS* 4.0 1.7 + - - +
139A SER* 3.1 26.0 - - - +
140A ILE 3.2 16.6 - - - +
141A PRO* 4.0 11.7 - - + -
142A GLN* 4.0 2.7 - - + +
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Residues in contact with LEU 133 (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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131A GLU 3.7 2.0 + - - +
132A PRO* 1.3 76.2 - - - +
134A LYS* 1.3 62.8 + - - +
135A VAL* 4.0 4.7 + - + -
138A LEU 3.6 0.9 - - - +
139A SER* 3.4 3.0 - - - -
140A ILE* 2.6 49.4 + - + +
142A GLN* 3.4 36.8 - - + +
19B GLU* 6.1 5.4 - - + -
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Residues in contact with LYS 134 (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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132A PRO 4.0 1.9 + - - +
133A LEU* 1.3 75.6 - - - +
135A VAL* 1.3 62.2 + - - +
136A GLY 3.6 24.1 + - - +
137A SER* 5.2 5.6 - - - +
138A LEU 3.5 9.0 - - - +
139A SER* 5.0 5.6 - - - +
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Residues in contact with VAL 135 (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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133A LEU* 5.0 5.2 - - + -
134A LYS* 1.3 76.6 - - - +
136A GLY* 1.3 65.2 + - - +
137A SER 3.2 1.0 + - - -
138A LEU* 2.9 24.6 + - + +
140A ILE* 3.5 29.8 - - + -
18B LEU* 3.9 31.4 - - + -
19B GLU* 3.9 10.8 - - + +
20B LEU* 3.9 21.8 - - + -
35B ALA* 3.3 14.9 - - + +
36B TYR* 4.6 0.9 - - + -
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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