Contacts of the strand formed by residues 154 - 165 (chain A) in PDB entry 2IBT
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 154 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A ALA* 4.0 3.4 - - - +
99A PHE 3.5 10.5 - - - +
100A ASP 4.3 1.3 - - - +
102A ILE* 3.6 25.1 - - + +
150A ALA 3.2 12.4 + - - +
151A VAL* 3.1 14.2 + - - +
152A ARG 4.3 1.2 - - - +
153A LEU* 1.3 78.1 - - - +
155A LYS* 1.3 64.8 + - - +
156A PRO* 3.9 1.7 - - - +
158A GLY 3.7 18.4 - - - +
159A VAL 3.3 35.4 - - - +
160A LEU* 4.0 6.7 - - + +
208A PHE* 3.9 30.7 - - + -
210A LYS* 3.0 29.4 + - + -
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Residues in contact with LYS 155 (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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41A GLY* 5.3 0.8 - - - -
42A ARG* 4.0 6.9 - - - +
97A GLU* 3.9 20.7 + - - -
98A ALA* 3.5 38.4 - - + +
99A PHE 2.9 15.4 + - - +
100A ASP* 2.6 42.5 + - - +
154A LEU* 1.3 78.3 - - - +
156A PRO* 1.4 75.9 - - + +
157A GLY 3.3 0.2 + - - -
158A GLY* 2.8 22.6 + - - +
210A LYS* 3.8 3.3 - - - +
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Residues in contact with PRO 156 (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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154A LEU 3.9 2.4 - - - +
155A LYS* 1.4 92.5 - - + +
157A GLY* 1.3 57.6 + - - +
158A GLY 3.3 2.3 + - - -
210A LYS* 3.9 12.5 - - + +
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Residues in contact with GLY 157 (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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155A LYS 3.3 0.2 + - - -
156A PRO* 1.3 69.9 - - - +
158A GLY* 1.3 66.0 + - - +
159A VAL* 4.1 2.4 - - - +
209A GLN* 3.2 20.6 + - - -
210A LYS 2.8 25.0 + - - -
211A SER* 4.0 14.3 - - - -
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Residues in contact with GLY 158 (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 PHE 4.5 1.6 - - - -
100A ASP* 3.4 16.6 - - - -
154A LEU* 3.7 14.5 - - - +
155A LYS* 2.8 20.4 + - - -
156A PRO 3.2 2.4 + - - -
157A GLY* 1.3 79.3 - - - +
159A VAL* 1.3 59.0 + - - -
209A GLN* 3.3 3.6 - - - -
210A LYS* 2.9 24.7 + - - +
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Residues in contact with VAL 159 (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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34A LEU 4.6 2.7 - - - +
36A GLU* 4.3 15.3 - - + +
100A ASP 3.0 9.1 + - - +
101A LEU* 3.2 19.1 - - + +
102A ILE 2.8 24.4 + - - -
154A LEU* 3.3 6.2 - - - +
157A GLY 4.1 3.8 - - - +
158A GLY* 1.3 78.8 - - - +
160A LEU* 1.3 71.2 + - - +
161A VAL* 3.9 17.0 - - + -
207A ARG* 3.7 33.7 - - + +
208A PHE 3.3 5.4 - - - +
209A GLN* 3.9 22.0 - - + +
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Residues in contact with LEU 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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102A ILE* 3.1 16.4 - - + +
147A LEU* 4.1 19.3 - - + +
150A ALA* 3.6 24.0 - - + -
151A VAL* 3.7 31.0 - - + +
154A LEU* 4.0 11.2 - - + +
159A VAL* 1.3 74.3 - - - +
161A VAL* 1.3 65.1 + - - +
162A PHE* 3.4 45.8 - - + +
181A LEU* 5.6 0.4 - - + -
206A ILE* 3.5 2.6 - - + +
207A ARG* 3.3 4.5 - - - -
208A PHE* 2.8 43.8 + - + +
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Residues in contact with VAL 161 (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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31A MET* 3.3 33.1 - - + +
34A LEU* 4.2 11.4 - - + +
35A ALA* 4.0 24.2 - - + -
101A LEU* 4.5 1.8 - - + -
102A ILE 2.9 9.9 + - - -
103A LEU* 3.2 9.5 - - + -
104A GLY 3.0 23.0 + - - -
159A VAL* 3.9 17.3 - - + -
160A LEU* 1.3 78.4 - - - +
162A PHE* 1.3 60.5 + - - +
205A VAL* 3.7 27.1 - - + -
206A ILE 3.3 4.9 - - - +
207A ARG* 4.2 6.3 - - + -
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Residues in contact with PHE 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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31A MET* 3.6 4.7 - - - -
46A PRO* 3.9 20.6 - - + -
102A ILE* 4.0 5.6 - - + -
103A LEU 3.9 6.5 - - - -
104A GLY 3.2 24.5 - - - -
106A PRO* 3.8 17.0 - - + -
146A PHE* 3.7 37.0 - + + -
147A LEU* 3.5 20.4 - - + -
150A ALA* 3.9 10.5 - - + -
160A LEU* 3.4 28.9 - - + -
161A VAL* 1.3 80.8 - - - +
163A VAL* 1.3 59.9 + - - +
164A VAL* 4.1 6.7 - - + -
204A VAL 4.0 0.2 - - - +
205A VAL* 3.3 4.9 - - - +
206A ILE* 3.0 45.1 + - + +
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Residues in contact with VAL 163 (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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23A THR* 4.4 6.5 - - + -
27A VAL* 4.4 1.8 - - + -
31A MET* 3.5 25.0 - - - +
104A GLY 3.2 4.4 + - - -
105A ASN* 3.6 34.1 - - + +
106A PRO* 3.3 10.9 - - - +
108A TYR* 2.8 13.2 + - - +
162A PHE* 1.3 72.6 - - - +
164A VAL* 1.3 71.0 + - - +
192A LEU* 4.4 13.2 - - + -
196A PHE* 3.9 21.5 - - + -
203A ALA* 4.0 14.4 - - + -
204A VAL 3.4 14.4 - - - +
205A VAL* 4.4 1.8 - - + +
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Residues in contact with VAL 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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106A PRO* 3.6 24.7 - - + -
108A TYR* 3.5 6.3 - - - -
143A TYR* 3.8 18.2 - - + -
147A LEU* 4.3 10.1 - - + -
162A PHE* 4.1 10.8 - - + -
163A VAL* 1.3 81.4 - - - +
165A PRO* 1.4 73.7 - - + +
168A TRP* 3.5 29.2 - - + +
203A ALA* 3.3 4.4 - - - -
204A VAL* 2.8 40.5 + - + +
206A ILE* 4.3 14.4 - - + -
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Residues in contact with PRO 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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108A TYR* 3.6 35.8 - - + -
143A TYR* 3.5 37.7 + - + -
164A VAL* 1.4 92.9 - - + +
166A ALA* 1.3 59.3 + - - +
167A THR* 3.2 15.3 - - + +
168A TRP* 3.1 24.9 + - - -
201A VAL* 3.5 21.3 - - + -
202A SER 3.4 7.6 - - - +
203A ALA* 4.3 0.7 - - - -
204A VAL* 3.9 0.2 - - - +
5B G 5.5 0.2 - - - +
6B 2PR 5.7 1.3 - - - -
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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