Contacts of the strand formed by residues 180 - 188 (chain A) in PDB entry 2XWB
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 GLY 180 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148A PRO* 3.8 10.3 - - - -
178A ASN 3.7 0.8 + - - -
179A MET* 1.3 75.8 - - - +
181A GLN* 1.3 63.3 + - - -
182A TRP* 3.3 7.2 + - - -
201A GLU* 4.7 4.5 - - - -
202A VAL 2.9 32.6 + - - -
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Residues in contact with GLN 181 (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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147A ASN 4.6 0.7 - - - +
148A PRO* 3.5 21.4 - - - +
180A GLY* 1.3 69.6 - - - -
182A TRP* 1.3 64.5 + - - +
183A LYS* 4.1 4.9 + - - +
199A GLU* 3.7 29.9 - - - +
200A PHE* 3.7 4.4 + - - -
201A GLU* 3.6 44.3 + - + +
584A ASN* 4.4 4.0 + - - +
586A LYS* 3.9 22.0 - - - +
587A ASN* 5.1 1.4 - - - +
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Residues in contact with TRP 182 (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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145A ILE* 4.0 7.6 - - + -
146A GLU 3.3 18.8 - - - -
147A ASN* 3.4 23.6 - - + -
148A PRO* 3.4 19.1 - - + +
153A VAL* 3.8 22.7 - - + -
171A TRP* 3.6 28.7 - + - -
177A VAL* 3.3 27.3 - - + +
178A ASN* 2.8 27.5 + - + -
180A GLY 3.5 9.6 - - - -
181A GLN* 1.3 75.8 - - - +
183A LYS* 1.3 59.8 + - - +
199A GLU* 3.4 6.8 - - - +
200A PHE* 3.0 51.9 + + + +
202A VAL* 3.3 27.4 - - + +
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Residues in contact with LYS 183 (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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145A ILE* 3.5 5.4 - - - +
146A GLU* 3.0 52.7 + - + +
147A ASN 5.6 0.9 - - - +
150A GLY* 6.0 1.4 - - - -
181A GLN 4.9 4.0 - - - +
182A TRP* 1.3 77.2 - - - +
184A ILE* 1.3 66.5 - - - +
185A ARG* 3.9 31.2 + - + +
197A SER* 4.2 14.8 - - - +
198A THR 3.7 9.0 - - - +
199A GLU* 3.9 26.8 + - + -
200A PHE* 4.5 0.9 - - - -
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Residues in contact with ILE 184 (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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110A ILE* 3.3 23.3 - - + +
112A THR* 3.9 23.3 - - + -
123A VAL* 4.4 4.0 - - + -
125A TYR* 4.0 42.2 - - + -
127A ILE* 5.4 0.7 - - + -
143A VAL* 4.6 5.6 - - + -
144A ASN 3.7 9.6 - - - +
145A ILE* 4.9 9.2 - - + -
171A TRP* 6.4 0.2 - - + -
183A LYS* 1.3 71.8 - - - +
185A ARG* 1.3 62.8 + - - +
186A ALA* 5.7 0.2 - - + -
197A SER* 3.3 2.9 - - - -
198A THR 2.8 34.4 + - - +
200A PHE* 3.4 34.5 - - + -
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Residues in contact with ARG 185 (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 VAL* 3.6 3.1 - - - +
144A ASN* 2.8 44.0 + - + +
146A GLU* 2.9 48.0 + - + -
183A LYS* 3.9 20.1 + - + +
184A ILE* 1.3 76.7 - - - +
186A ALA* 1.3 64.3 + - - +
187A TYR* 5.4 2.2 - - + -
195A VAL* 3.9 26.9 - - + +
196A PHE 3.4 4.5 - - - +
197A SER* 3.2 17.8 + - - +
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Residues in contact with ALA 186 (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 LEU* 4.1 9.0 - - + -
110A ILE* 4.0 19.7 - - + -
127A ILE* 4.7 5.8 - - + -
141A VAL* 4.3 7.6 - - + -
142A MET 3.2 13.5 - - - +
143A VAL* 4.2 12.8 - - + -
184A ILE* 5.7 0.2 - - + -
185A ARG* 1.3 77.2 - - - +
187A TYR* 1.3 67.1 + - - +
195A VAL* 3.6 2.1 - - - +
196A PHE* 2.7 42.6 + - + +
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Residues in contact with TYR 187 (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 LEU* 3.6 12.7 - - - +
141A VAL* 3.5 0.9 - - - +
142A MET* 2.8 73.3 + - + +
144A ASN* 4.8 18.7 + - - -
185A ARG* 5.4 1.8 - - + -
186A ALA* 1.3 83.2 - - - +
188A TYR* 1.3 82.4 + - - +
189A GLU* 4.9 2.5 - - - -
191A SER 4.0 1.1 - - - +
192A PRO* 3.5 28.8 - - + +
194A GLN 3.3 22.4 - - - +
195A VAL* 4.0 20.2 - - + -
196A PHE* 4.7 0.4 - - - -
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Residues in contact with TYR 188 (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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105A SER* 3.7 25.1 - - - +
106A GLY* 3.9 20.9 - - - -
107A TYR 3.0 13.2 + - - -
108A LEU* 3.4 28.7 - - + -
129A THR* 3.4 8.0 - - - -
130A VAL 3.0 31.9 + - - -
137A VAL* 4.6 1.0 - - + +
139A ARG* 3.4 42.0 - - + -
140A THR 3.7 7.6 - - - -
141A VAL* 4.2 7.2 - - + +
187A TYR* 1.3 90.5 - - - +
189A GLU* 1.3 63.7 + - - +
190A ASN* 3.1 2.5 - - + +
191A SER* 3.1 28.3 + - - +
194A GLN* 4.7 1.1 + - - -
196A PHE* 4.7 7.0 - + - -
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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