Contacts of the strand formed by residues 157 - 168 (chain A) in PDB entry 3IND
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 VAL 157 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146A LEU* 3.4 5.6 - - - -
147A VAL* 2.7 34.6 + - + +
155A VAL* 4.4 1.8 - - + -
156A THR* 1.3 79.4 - - - +
158A ARG* 1.3 60.2 + - - +
159A ALA* 3.5 8.8 + - + -
198A PHE* 3.7 32.3 - - + -
201A SER 4.7 0.7 - - - +
202A LEU* 3.7 29.6 - - + +
205A GLN* 3.5 17.7 - - + +
206A THR* 3.5 30.3 - - + -
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Residues in contact with ARG 158 (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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121A THR* 2.7 45.2 + - - +
123A ARG* 3.4 49.3 - - - +
144A THR* 2.7 57.7 + - + -
145A ASP* 3.4 6.5 - - - +
146A LEU* 3.8 24.1 - - + +
157A VAL* 1.3 70.5 - - - +
159A ALA* 1.3 60.3 + - - +
201A SER* 4.1 2.9 + - - -
205A GLN* 2.6 41.3 + - - +
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Residues in contact with ALA 159 (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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100A PHE* 4.8 0.4 - - + -
144A THR* 3.2 24.1 - - - -
145A ASP 3.1 12.0 + - - +
147A VAL* 4.2 11.2 - - + -
157A VAL* 3.5 5.7 + - + -
158A ARG* 1.3 76.7 - - - +
160A ASN* 1.3 70.2 + - - +
161A ILE* 3.6 2.9 + - - +
198A PHE* 3.6 36.8 - - + -
201A SER* 4.4 11.4 - - - -
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Residues in contact with ASN 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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100A PHE* 3.4 22.5 + - - +
125A LEU* 3.7 7.8 - - + +
142A LEU* 5.8 0.4 - - + -
143A GLY 3.5 4.5 - - - +
144A THR* 3.5 18.4 - - - +
159A ALA* 1.3 75.5 - - - +
161A ILE* 1.3 63.3 + - - +
195A LEU* 3.4 33.7 - - + +
196A GLU* 2.9 50.6 + - - +
198A PHE* 5.7 1.3 - - - +
201A SER* 4.8 2.8 + - - -
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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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82A VAL* 3.4 31.6 - - + -
100A PHE* 3.6 24.0 - - + +
102A VAL* 4.4 9.0 - - + -
114A TYR* 3.9 25.8 - - + +
122A TYR* 6.0 1.2 - - + -
141A GLU 3.5 1.2 - - - +
142A LEU* 3.8 4.5 - - - -
143A GLY* 2.7 35.9 + - - +
144A THR 4.7 0.2 - - - -
145A ASP* 3.6 23.1 - - + +
147A VAL* 3.9 12.1 - - + -
159A ALA 3.7 7.0 - - - +
160A ASN* 1.3 80.5 - - - +
162A ALA* 1.3 71.6 + - - +
163A ALA* 3.5 4.3 + - + +
195A LEU* 6.3 0.2 - - - -
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Residues in contact with ALA 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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99A ASN* 4.9 7.0 - - - +
100A PHE 2.8 17.8 + - - +
101A ALA* 3.3 3.6 - - + +
102A VAL 2.9 28.6 + - - -
129A VAL* 4.3 9.4 - - + -
138A TRP* 3.4 35.7 - - + -
141A GLU 3.9 4.3 - - - -
142A LEU* 4.4 8.5 - - + +
160A ASN 4.3 0.2 - - - -
161A ILE* 1.3 72.6 - - - +
163A ALA* 1.3 59.5 + - - +
164A ILE 3.3 3.0 + - - -
195A LEU* 5.9 0.6 - - + +
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Residues in contact with ALA 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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102A VAL 3.6 5.4 - - - -
104A ALA* 3.4 20.0 - - + -
114A TYR* 4.5 8.1 - - + -
116A ARG* 3.7 30.3 - - - +
122A TYR* 5.9 0.4 - - + -
140A GLY* 3.0 4.6 - - - -
141A GLU 3.0 37.7 + - - +
161A ILE* 3.5 4.9 + - - +
162A ALA* 1.3 68.3 - - - +
164A ILE* 1.3 64.2 + - - +
165A THR* 3.2 5.7 + - - +
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Residues in contact with ILE 164 (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 ALA* 3.9 12.3 - - + +
102A VAL 2.8 40.3 + - - +
103A GLY* 3.9 3.5 - - - +
104A ALA 2.9 23.6 + - - -
105A ALA 3.5 5.5 + - - +
138A TRP* 3.7 21.8 - - + -
139A GLU 3.4 7.4 - - - +
140A GLY* 4.1 0.4 - - - -
162A ALA 4.0 2.0 - - - +
163A ALA* 1.3 67.7 - - - +
165A THR* 1.3 62.1 + - - +
166A GLU 3.6 21.3 - - - +
167A SER* 4.0 15.9 - - - -
170A PHE* 3.5 31.0 - - + -
171A PHE* 3.8 15.1 - - + -
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Residues in contact with THR 165 (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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104A ALA 4.8 0.9 - - - +
105A ALA* 3.7 25.4 - - + +
106A PRO 5.4 1.4 - - - +
116A ARG* 3.6 27.8 - - - +
139A GLU* 3.0 19.6 + - - +
140A GLY* 4.1 5.7 - - - -
141A GLU* 4.3 17.1 + - + +
163A ALA 3.2 10.9 + - - +
164A ILE* 1.3 75.0 - - - +
166A GLU* 1.3 67.0 + - - +
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Residues in contact with GLU 166 (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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107A HIS* 5.3 5.9 - - - -
137A LYS* 6.4 2.0 - - - -
138A TRP* 3.5 0.3 - - - -
139A GLU* 2.7 52.1 + - + +
164A ILE* 3.6 2.8 - - - +
165A THR* 1.3 84.8 + - - +
167A SER* 1.3 81.5 + - - +
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Residues in contact with SER 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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107A HIS* 3.9 16.5 + - - -
137A LYS* 3.4 15.5 - - - +
138A TRP* 3.8 12.3 - - - +
164A ILE* 4.0 7.2 - - - -
166A GLU* 1.3 98.6 + - - +
168A ASP* 1.3 62.4 + - - +
170A PHE* 3.9 11.2 + - - +
171A PHE* 3.3 27.1 + - - -
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Residues in contact with ASP 168 (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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136A GLY* 3.4 5.0 - - - -
137A LYS* 2.9 51.5 + - + +
167A SER* 1.3 75.1 - - - +
169A LYS* 1.3 103.8 + - - +
170A PHE 3.0 2.0 + - - -
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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