Contacts of the strand formed by residues 123 - 135 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119B ARG* 3.6 4.8 - - - +
120B LEU* 2.7 39.6 + - + +
121B PRO 3.7 0.6 - - - -
122B GLY* 1.3 82.5 - - - +
124B VAL* 1.3 58.4 + - - +
125B VAL* 5.2 0.4 - - - -
147B VAL* 4.1 15.5 - - + -
148B GLU 3.0 16.4 - - - +
149B GLY* 4.0 2.0 - - - -
152B ALA* 4.1 4.7 - - - -
155B TRP* 3.7 23.3 - - + -
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Residues in contact with VAL 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B GLU* 4.0 16.4 - - - +
117B VAL* 4.0 15.5 - - + -
118B TYR 3.4 11.4 - - - +
119B ARG* 4.4 3.6 - - + +
123B ALA* 1.3 74.1 - - - +
125B VAL* 1.3 63.5 + - - +
126B ARG* 4.0 23.7 + - + +
146B GLU 3.7 1.0 - - - +
147B VAL* 3.5 3.6 - - - -
148B GLU* 2.7 56.2 + - + +
149B GLY* 5.6 0.2 - - - -
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Residues in contact with VAL 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B LEU* 5.1 1.3 - - + -
105B LEU* 4.3 15.9 - - + -
116B GLY 3.6 1.2 - - - +
117B VAL* 3.4 5.0 - - - +
118B TYR* 2.7 42.0 + - + +
120B LEU* 3.7 30.7 - - + -
123B ALA 5.2 0.2 - - - -
124B VAL* 1.3 76.0 - - - +
126B ARG* 1.3 64.0 + - - +
127B PHE* 4.2 15.5 + - + -
145B VAL* 3.9 16.4 - - + -
146B GLU 3.5 3.4 - - - +
147B VAL* 4.4 11.0 - - + -
155B TRP* 5.3 0.2 - - + -
159B ILE* 3.9 28.9 - - + -
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Residues in contact with ARG 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B GLY 3.2 8.1 - - - +
117B VAL* 3.4 32.5 - - + +
124B VAL* 4.4 24.5 - - + +
125B VAL* 1.3 77.6 - - - +
127B PHE* 1.3 61.6 + - - +
144B ARG 3.8 0.7 - - - +
145B VAL* 3.5 1.0 - - - +
146B GLU* 2.6 67.7 + - + +
148B GLU* 5.2 13.8 + - - -
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Residues in contact with PHE 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B PRO* 4.5 11.0 - - + -
101B LEU* 3.7 19.1 - - + -
102B GLU* 3.7 37.0 - - + -
105B LEU* 3.9 11.9 - - + -
115B GLU* 5.7 0.4 - - - -
116B GLY* 3.0 43.1 + - - +
118B TYR* 3.6 26.0 - + - -
125B VAL* 4.2 10.8 - - + -
126B ARG* 1.3 78.1 - - - +
128B ARG* 1.3 65.8 + - - +
143B LEU* 4.3 15.0 - - + -
144B ARG 3.1 10.8 - - - +
145B VAL* 4.0 17.5 - - + -
146B GLU* 5.8 0.2 - - - -
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Residues in contact with ARG 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B PHE* 1.3 78.4 - - - +
129B GLU* 1.3 78.1 + - + +
130B VAL* 3.6 5.3 + - + +
143B LEU* 3.6 6.9 - - - +
144B ARG* 2.9 34.9 + - + +
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Residues in contact with GLU 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B PHE 4.8 1.0 - - - +
98B PRO* 3.3 33.7 - - + +
128B ARG* 1.3 93.2 + - + +
130B VAL* 1.3 64.8 + - - +
141B PRO* 4.1 13.7 - - - +
142B GLN 3.2 28.9 + - - +
143B LEU* 4.0 13.8 - - + +
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Residues in contact with VAL 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B THR* 4.0 13.2 - - + +
128B ARG* 3.9 6.1 - - + +
129B GLU* 1.3 82.6 - - - +
131B GLU* 1.3 70.6 + - - +
132B PRO* 3.2 7.4 - - - +
142B GLN* 2.8 41.7 + - + +
144B ARG* 3.9 29.2 - - + +
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Residues in contact with GLU 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B VAL* 1.3 76.6 - - - +
132B PRO* 1.3 88.6 - - - +
133B LEU* 4.7 3.1 - - - +
142B GLN* 3.2 17.5 - - - +
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Residues in contact with PRO 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B VAL 3.2 7.6 - - - +
131B GLU* 1.3 109.8 - - - +
133B LEU* 1.3 64.3 + - - +
134B LYS* 5.3 0.5 - - - +
139B SER* 3.5 23.6 - - - +
140B ILE 3.3 17.7 - - - +
141B PRO* 4.2 7.0 - - + -
142B GLN* 3.9 3.6 - - + +
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Residues in contact with LEU 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B GLU 4.7 2.7 - - - +
132B PRO* 1.3 78.5 - - - +
134B LYS* 1.3 63.1 + - - +
135B VAL* 4.3 2.5 - - + -
139B SER* 3.5 5.9 + - - -
140B ILE* 2.8 46.9 + - + +
142B GLN* 3.4 37.7 - - + +
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Residues in contact with LYS 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B PRO 5.3 0.4 - - - +
133B LEU* 1.3 77.5 - - - +
135B VAL* 1.3 65.7 + - - +
136B GLY 2.8 25.8 + - - +
137B SER* 3.7 16.0 + - - +
138B LEU 3.3 19.5 - - - +
139B SER* 4.2 9.6 - - - +
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Residues in contact with VAL 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LEU* 4.0 26.7 - - + -
19A GLU* 3.7 15.3 - - + +
20A LEU* 3.9 21.5 - - + -
35A ALA* 3.2 10.2 - - + +
36A TYR* 4.3 5.6 - - + -
133B LEU* 5.4 2.9 - - + -
134B LYS* 1.3 78.5 - - - +
136B GLY* 1.3 67.2 + - - +
137B SER 3.2 0.5 + - - -
138B LEU* 2.9 23.5 + - + +
140B ILE* 3.6 28.7 - - + +
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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