Contacts of the strand formed by residues 140 - 150 (chain B) in PDB entry 3Q2S
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 140 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122B LYS* 5.5 0.2 - - - +
139B TRP* 1.3 77.2 - - - +
141B ILE* 1.3 64.5 + - - +
142B ASP* 4.1 13.7 - - - +
177B VAL* 3.7 1.1 - - - +
178B GLN* 2.9 69.3 + - + +
179B LEU 6.0 0.2 - - - -
180B GLN* 4.5 22.4 - - + +
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Residues in contact with ILE 141 (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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33A LEU* 4.2 7.2 - - + +
118B VAL* 3.9 26.4 - - + +
121B LEU* 3.7 35.4 - - + -
122B LYS* 4.0 23.5 - - + +
125B MET* 5.1 1.6 - - + -
139B TRP* 3.8 9.2 + - + +
140B VAL* 1.3 83.5 - - - +
142B ASP* 1.3 66.0 + - - +
143B ASP 4.7 1.3 - - - +
175B PHE* 3.7 37.2 - - + -
176B LEU 4.1 6.7 - - - +
177B VAL* 4.2 17.5 - - + -
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Residues in contact with ASP 142 (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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30A PRO* 5.3 0.2 - - - +
32A THR* 2.4 38.1 + - - +
33A LEU* 3.7 10.8 + - - +
35B ARG* 3.6 17.5 + - - +
140B VAL* 4.1 11.5 + - - +
141B ILE* 1.3 85.1 + - - +
143B ASP* 1.3 69.5 + - - +
176B LEU 4.2 3.0 + - - -
178B GLN* 4.2 15.0 + - - +
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Residues in contact with ASP 143 (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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32A THR* 3.1 10.8 - - - +
33A LEU* 4.1 1.7 - - - +
35B ARG* 2.9 52.7 + - - +
37B ILE* 4.5 5.3 - - - +
141B ILE 3.7 1.2 - - - -
142B ASP* 1.3 88.4 + - - +
144B CYS* 1.3 58.9 + - - +
175B PHE* 3.2 15.1 - - - +
176B LEU* 3.0 47.5 + - + +
178B GLN* 4.6 2.6 + - - -
221B ARG* 4.6 4.3 + - - +
222B PHE* 3.8 15.9 - - + -
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Residues in contact with CYS 144 (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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32A THR 3.2 8.9 + - - +
33A LEU* 3.5 23.7 - - - +
34A GLU* 5.6 0.2 - - - -
221A ARG* 3.8 31.4 + - + +
143B ASP* 1.3 73.0 - - - +
145B ILE* 1.3 63.2 + - - +
146B GLY 3.7 24.2 - - - -
147B ASN* 4.5 0.7 - - - -
173B LYS* 3.9 22.4 - - - -
174B LEU 3.6 7.2 - - - +
175B PHE* 4.1 9.4 - - + -
221B ARG* 3.3 17.3 + - - -
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Residues in contact with ILE 145 (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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217A GLN 4.8 1.9 - - - +
221A ARG* 3.6 18.4 - - - +
83B VAL* 3.6 22.4 - - + -
143B ASP 4.2 0.2 - - - +
144B CYS* 1.3 75.5 - - - +
146B GLY* 1.3 63.8 + - - +
174B LEU* 2.9 19.5 + - + -
175B PHE 3.9 1.1 - - - -
176B LEU* 3.4 36.3 - - + +
215B LEU* 3.4 31.6 - - + -
218B LEU* 4.1 38.2 - - + +
219B LEU* 4.7 8.7 - - + -
221B ARG* 4.6 2.9 + - - +
222B PHE* 4.6 12.6 - - + -
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Residues in contact with GLY 146 (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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220A SER* 3.5 10.5 - - - -
221A ARG* 4.0 5.4 - - - -
144B CYS* 3.7 6.7 - - - -
145B ILE* 1.3 88.7 - - - +
147B ASN* 1.3 71.0 + - - +
148B TRP* 4.7 4.5 - - - -
174B LEU* 3.0 27.2 + - - -
218B LEU* 5.0 5.8 - - - -
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Residues in contact with ASN 147 (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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220A SER* 2.7 40.4 + - - +
221A ARG* 3.7 17.0 + - - +
222A PHE 5.0 2.4 + - - -
144B CYS* 4.5 1.0 - - - -
146B GLY* 1.3 73.4 - - - -
148B TRP* 1.3 70.0 + - - +
149B TRP* 3.4 23.3 - - + -
159B PRO* 3.5 12.0 - - - +
171B HIS* 2.9 26.9 + - - +
172B LYS 3.2 4.9 - - - -
173B LYS* 3.2 31.7 - - - +
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Residues in contact with TRP 148 (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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202A TYR* 3.7 20.0 - + - -
217A GLN* 4.0 21.5 - - + +
220A SER* 4.7 3.0 + - - -
146B GLY 5.2 0.2 - - - -
147B ASN* 1.3 97.2 + - - +
149B TRP* 1.3 62.0 + - - +
157B GLN* 3.7 22.7 - - + +
158B TYR 3.4 17.7 - - - -
159B PRO* 3.5 23.6 - - + -
170B GLU 3.9 0.5 - - - +
171B HIS* 3.6 1.6 - - - -
172B LYS* 2.7 53.8 + - + +
174B LEU* 4.2 12.5 - - + +
210B PRO* 3.5 26.0 - - + -
211B ILE* 3.8 38.6 - - + +
214B SER* 3.5 21.7 + - - -
218B LEU* 4.9 8.1 - - - +
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Residues in contact with TRP 149 (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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220A SER* 4.1 8.1 - - - -
222A PHE 5.8 2.0 - - - -
76B MET* 3.7 26.1 - - + +
147B ASN* 3.4 31.6 - - + -
148B TRP* 1.3 76.1 - - - +
150B ARG* 1.3 60.5 + - - +
151B PRO* 3.5 6.1 - - + +
157B GLN* 3.3 3.4 - - - -
158B TYR* 2.7 37.9 + - - +
159B PRO 3.1 24.2 - - - -
160B TYR* 3.4 34.0 - - - +
161B ILE* 3.8 32.8 - - + +
162B PRO* 5.9 0.7 - - + -
168B PRO* 4.1 12.1 - - + -
170B GLU 3.3 3.6 - - - -
171B HIS* 3.7 25.4 + + - +
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Residues in contact with ARG 150 (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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63B ARG* 3.3 32.0 - - - +
64B PHE* 3.9 16.1 - - - -
67B MET* 4.1 9.8 - - - +
149B TRP* 1.3 72.8 - - - +
151B PRO* 1.3 58.4 - - + +
152B ASN 3.3 14.7 + - - +
154B GLU 3.0 28.2 + - - +
155B PRO* 2.6 38.3 + - - +
156B PRO 3.4 10.3 - - - +
157B GLN* 3.6 30.0 + - - +
168B PRO* 3.6 2.2 - - - -
169B LYS* 2.8 33.0 + - - +
170B GLU* 2.9 44.9 + - + -
172B LYS* 4.7 3.2 - - - +
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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