Contacts of the strand formed by residues 140 - 150 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138A ASP* 4.3 3.8 + - + +
139A TRP* 1.3 70.3 - - - +
141A ILE* 1.3 61.5 + - - +
142A ASP* 4.1 12.9 + - + +
176A LEU 4.1 0.9 - - - +
177A VAL* 3.7 1.6 - - - +
178A GLN* 2.9 71.7 + - + +
180A GLN* 5.1 10.9 + - + +
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Residues in contact with ILE 141 (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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118A VAL* 3.3 31.7 - - + +
121A LEU* 3.6 31.9 - - + -
122A LYS* 3.9 29.2 - - + +
125A MET* 5.1 1.8 - - + -
139A TRP* 3.5 16.9 + - + +
140A VAL* 1.3 74.0 - - - +
142A ASP* 1.3 61.3 + - - +
175A PHE* 3.5 34.8 - - + -
176A LEU 3.9 4.9 - - - +
177A VAL* 3.9 16.8 - - + -
33B LEU* 4.0 6.1 - - + +
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Residues in contact with ASP 142 (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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35A ARG* 3.2 18.8 + - - -
140A VAL* 4.1 11.6 - - + +
141A ILE* 1.3 75.7 - - - +
143A ASP* 1.3 84.5 + - - +
176A LEU 4.1 1.8 + - - +
178A GLN* 2.7 22.7 + - - +
30B PRO* 5.3 5.4 - - + -
32B THR* 2.4 34.4 + - - +
33B LEU* 3.1 23.3 - - + +
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Residues in contact with ASP 143 (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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35A ARG* 2.7 38.3 + - - +
37A ILE* 4.9 0.7 - - - +
142A ASP* 1.3 110.8 + - - +
144A CYS* 1.3 58.9 + - - +
175A PHE* 3.0 6.1 - - - +
176A LEU* 2.7 50.1 + - + +
178A GLN* 3.9 1.4 + - - -
221A ARG* 4.6 3.5 + - - +
222A PHE* 3.8 22.1 - - + -
32B THR* 3.4 15.8 - - - +
33B LEU* 3.4 5.5 - - - +
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Residues in contact with CYS 144 (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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143A ASP* 1.3 74.4 - - - +
145A ILE* 1.3 63.0 + - - +
146A GLY 3.8 9.0 - - - -
147A ASN* 4.0 10.8 - - - -
173A LYS* 3.2 41.5 - - - -
174A LEU 3.3 7.2 - - - +
175A PHE* 3.9 10.1 - - + -
221A ARG* 3.8 15.4 + - - -
32B THR 3.4 8.7 + - - +
33B LEU* 3.4 22.7 - - - +
221B ARG* 4.0 20.3 + - - +
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Residues in contact with ILE 145 (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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83A VAL* 3.6 34.3 - - + -
143A ASP 4.0 0.7 - - - +
144A CYS* 1.3 79.0 - - - +
146A GLY* 1.3 56.0 + - - +
174A LEU* 2.6 28.8 + - + +
176A LEU* 3.7 30.3 - - + +
215A LEU* 4.3 8.3 - - + -
218A LEU* 3.4 38.1 - - + +
219A LEU* 3.9 18.6 - - + -
221A ARG* 4.9 1.5 + - - +
222A PHE* 4.0 20.2 - - + -
221B ARG* 3.8 18.1 + - - +
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Residues in contact with GLY 146 (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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144A CYS* 3.7 2.6 - - - -
145A ILE* 1.3 84.3 - - - +
147A ASN* 1.3 66.9 + - - -
148A TRP* 4.6 6.7 - - - -
172A LYS 4.0 0.2 - - - +
173A LYS* 3.5 4.7 - - - +
174A LEU* 2.9 29.7 + - - +
218A LEU* 5.1 4.9 - - - -
217B GLN 5.1 0.2 - - - -
220B SER* 3.5 12.1 - - - -
221B ARG* 4.0 6.7 - - - -
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Residues in contact with ASN 147 (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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144A CYS* 4.0 7.1 - - - -
146A GLY* 1.3 77.0 + - - -
148A TRP* 1.3 72.7 + - - +
149A TRP* 3.5 25.1 - - + -
159A PRO* 3.5 6.9 - - - +
171A HIS* 2.8 28.2 + - - +
172A LYS 3.2 4.7 - - - -
173A LYS* 3.2 22.8 + - - +
220B SER* 2.7 44.2 + - - +
221B ARG* 3.5 14.8 + - - +
222B PHE 5.2 0.4 + - - -
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Residues in contact with TRP 148 (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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146A GLY* 4.6 3.5 - - - -
147A ASN* 1.3 95.4 + - - +
149A TRP* 1.3 62.6 + - - +
157A GLN* 3.3 32.0 - - + +
158A TYR* 3.3 18.6 - - - -
159A PRO* 3.5 26.3 - - + +
170A GLU 3.9 0.5 - - - +
171A HIS* 3.7 2.1 - - - -
172A LYS* 2.8 44.3 + - + +
174A LEU* 4.9 6.8 - - + +
210A PRO* 4.0 20.0 - - + -
211A ILE* 3.7 48.4 - - + +
214A SER* 3.8 21.2 + - - -
218A LEU* 4.8 9.1 - - - +
202B TYR* 3.8 20.0 - + - -
217B GLN* 4.0 15.4 - - + +
220B SER* 4.7 4.0 + - - -
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Residues in contact with TRP 149 (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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76A MET* 5.0 3.3 - - - +
147A ASN* 3.5 21.8 - - + -
148A TRP* 1.3 76.5 - - - +
150A ARG* 1.3 60.7 + - - +
151A PRO* 3.3 7.9 - - + +
157A GLN* 3.5 4.0 - - - -
158A TYR* 3.0 30.7 + - - +
159A PRO 3.5 18.6 - - - -
160A TYR* 3.5 31.8 - - - +
161A ILE* 3.4 39.7 - - + +
162A PRO* 5.6 1.3 - - + -
168A PRO* 4.2 15.7 - - + -
170A GLU 3.5 3.6 - - - -
171A HIS* 3.2 50.0 + + + -
220B SER* 4.4 8.3 - - - -
222B PHE 5.8 1.8 - - - -
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Residues in contact with ARG 150 (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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63A ARG* 4.4 15.6 - - - +
64A PHE* 4.1 10.8 - - - -
67A MET* 4.0 19.9 - - - -
149A TRP* 1.3 71.3 - - - +
151A PRO* 1.3 65.2 - - - +
152A ASN 3.3 14.1 - - - +
154A GLU 2.9 36.1 + - - +
155A PRO* 3.1 24.9 + - - +
156A PRO 3.4 8.5 - - - +
157A GLN* 3.1 29.3 + - + +
168A PRO* 3.9 2.4 - - - -
169A LYS* 2.9 28.2 + - - +
170A GLU* 2.8 50.5 + - + +
172A LYS* 5.1 4.2 - - - +
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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