Contacts of the strand formed by residues 154 - 165 (chain D) in PDB entry 2IBS
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98D ALA* 3.8 5.4 - - - +
99D PHE 3.6 13.7 - - - +
100D ASP 4.3 0.7 - - - +
102D ILE* 3.7 26.7 - - + +
150D ALA 3.4 6.5 - - - +
151D VAL* 3.2 13.5 - - - +
152D ARG 3.2 2.6 - - - +
153D LEU* 1.3 79.0 - - - +
155D LYS* 1.3 62.3 + - - +
156D PRO* 4.0 1.6 - - - +
158D GLY* 3.4 30.1 - - - +
159D VAL 3.6 29.6 - - - +
160D LEU* 4.0 7.0 - - + -
208D PHE* 4.0 24.5 - - + -
210D LYS* 3.2 25.5 + - + +
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Residues in contact with LYS 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D ARG* 4.1 5.7 - - - +
97D GLU* 2.9 33.0 + - - -
98D ALA* 3.5 32.6 - - + +
99D PHE 2.8 17.3 + - - +
100D ASP* 3.7 35.2 + - - +
154D LEU* 1.3 76.0 - - - +
156D PRO* 1.4 74.8 - - + +
157D GLY 3.2 0.3 + - - -
158D GLY* 2.8 23.1 + - - +
210D LYS* 3.6 7.8 - - - +
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Residues in contact with PRO 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D ALA* 5.8 0.2 - - + -
154D LEU 4.5 1.6 - - - +
155D LYS* 1.4 92.3 - - + +
157D GLY* 1.3 59.9 + - - +
158D GLY 3.5 0.2 + - - -
210D LYS* 4.0 12.3 - - + +
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Residues in contact with GLY 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156D PRO* 1.3 71.6 - - - +
158D GLY* 1.3 64.7 + - - +
159D VAL* 3.9 3.1 + - - +
209D GLN* 3.3 21.4 + - - -
210D LYS 3.1 18.0 + - - -
211D SER* 4.0 17.4 - - - -
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Residues in contact with GLY 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D PHE 4.4 1.8 - - - -
100D ASP* 3.4 17.0 - - - -
154D LEU* 3.4 15.6 - - - +
155D LYS* 2.8 20.0 + - - -
156D PRO 3.2 1.6 + - - -
157D GLY* 1.3 79.3 - - - +
159D VAL* 1.3 60.0 + - - -
209D GLN* 3.3 4.5 - - - -
210D LYS* 2.9 24.0 + - - +
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Residues in contact with VAL 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D GLU* 3.9 29.6 - - + +
100D ASP 2.9 10.1 + - - +
101D LEU* 3.3 11.8 - - + +
102D ILE 3.0 23.9 + - - -
154D LEU* 3.6 5.2 - - - +
157D GLY 4.1 8.1 - - - +
158D GLY* 1.3 77.5 - - - +
160D LEU* 1.3 63.1 + - - +
161D VAL* 4.0 21.3 - - + -
207D ARG* 3.7 35.4 - - + +
208D PHE 3.3 7.0 - - - +
209D GLN* 4.2 11.9 - - + +
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Residues in contact with LEU 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D ILE* 3.3 8.5 - - + +
147D LEU* 4.0 26.9 - - + +
150D ALA* 3.6 31.6 - - + -
151D VAL* 3.9 26.9 - - + +
154D LEU* 4.0 9.6 - - + -
159D VAL* 1.3 74.0 - - - +
161D VAL* 1.3 66.4 + - - +
162D PHE* 4.0 13.5 - - + +
181D LEU* 5.8 0.2 - - + -
206D ILE* 3.3 15.8 - - + +
207D ARG* 3.2 6.6 - - - +
208D PHE* 2.6 56.2 + - + +
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Residues in contact with VAL 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D MET* 3.4 35.4 - - + +
34D LEU* 4.2 5.6 - - + +
35D ALA* 3.9 29.2 - - + +
101D LEU* 4.4 2.2 - - + -
102D ILE 2.9 10.1 + - - -
103D LEU* 3.2 29.0 - - + -
104D GLY 3.2 5.5 + - - -
159D VAL* 4.0 12.1 - - + -
160D LEU* 1.3 78.2 - - - +
162D PHE* 1.3 60.5 + - - +
205D VAL* 3.9 24.0 - - + -
206D ILE 3.3 4.0 - - - +
207D ARG* 4.1 10.8 - - + -
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Residues in contact with PHE 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D MET* 3.6 4.0 - - - -
46D PRO* 3.8 23.8 - - + -
102D ILE* 3.8 20.6 - - + -
103D LEU* 4.0 2.7 - - - -
104D GLY* 3.5 23.3 - - - -
106D PRO* 3.9 17.9 - - + -
146D PHE* 3.7 34.3 - + + -
147D LEU* 3.8 19.7 - - + -
150D ALA* 3.9 17.3 - - + -
160D LEU* 4.0 7.1 - - + +
161D VAL* 1.3 85.7 - - - +
163D VAL* 1.3 61.8 + - - +
164D VAL* 4.1 6.3 - - + -
205D VAL* 3.4 5.4 - - - +
206D ILE* 2.9 47.4 + - + +
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Residues in contact with VAL 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D THR* 4.4 9.4 - - + -
27D VAL* 4.2 12.8 - - + -
31D MET* 3.5 26.0 - - + +
104D GLY 3.3 4.0 + - - -
105D ASN* 3.4 37.0 + - + +
106D PRO* 3.5 2.9 - - - +
108D TYR* 2.6 19.6 + - - +
162D PHE* 1.3 72.1 - - - +
164D VAL* 1.3 65.1 + - - +
192D LEU* 4.4 1.8 - - + -
196D PHE* 3.9 21.3 - - + -
203D ALA* 4.2 11.0 - - + -
204D VAL 3.5 10.5 - - - +
205D VAL* 4.4 6.5 - - + -
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Residues in contact with VAL 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D PRO* 3.8 21.5 - - + -
108D TYR* 3.6 4.7 - - - -
143D TYR* 3.7 23.3 - - + +
147D LEU* 4.6 9.0 - - + -
162D PHE* 4.3 10.8 - - + -
163D VAL* 1.3 79.2 - - - +
165D PRO* 1.4 73.0 - - + +
168D TRP* 3.6 28.0 - - + +
203D ALA* 3.4 6.6 - - - +
204D VAL* 2.8 38.5 + - + +
206D ILE* 4.1 15.7 - - + -
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Residues in contact with PRO 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D TYR* 3.5 40.4 - - + -
141D ASN* 6.0 0.2 - - - +
143D TYR* 3.7 26.7 + - + -
164D VAL* 1.4 94.6 - - + +
166D ALA* 1.3 58.9 + - - +
167D THR* 3.1 19.0 + - + +
168D TRP* 3.1 24.9 + - - -
201D VAL* 3.8 18.4 - - + -
202D SER 3.4 7.9 - - - +
204D VAL* 3.8 0.4 - - - +
5E G 5.5 0.2 - - - +
6E 2PR 5.9 1.6 - - - -
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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