Contacts of the strand formed by residues 152 - 159 (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 PRO 152 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A ASN* 4.8 23.1 - - + +
145A ILE 3.5 9.0 - - - +
146A GLU* 3.9 19.7 - - + +
150A GLY 3.9 6.1 - - - +
151A ILE* 1.3 86.9 - - + +
153A VAL* 1.3 58.5 + - - +
154A LYS 4.9 2.0 - - - +
155A GLN* 5.8 0.9 - - + -
1295B SER* 3.6 24.5 - - - +
1296B LEU* 3.9 14.8 - - + -
1297B LEU* 2.9 30.5 + - - +
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Residues in contact with VAL 153 (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* 2.9 29.8 + - + +
147A ASN* 4.3 4.7 - - + +
151A ILE 3.5 15.0 - - - +
152A PRO* 1.3 72.2 - - - +
154A LYS* 1.3 64.9 + - + +
155A GLN* 4.9 0.2 - - - +
171A TRP* 4.4 10.3 - - + +
182A TRP* 3.8 29.6 - - + -
1296B LEU* 4.2 4.3 - - - +
1297B LEU* 3.6 41.7 - - + +
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Residues in contact with LYS 154 (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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125A TYR* 4.6 7.8 + - - -
143A VAL* 3.8 0.6 - - - +
144A ASN* 3.3 3.8 - - - +
145A ILE* 3.0 38.9 + - + +
152A PRO* 3.7 1.4 - - - +
153A VAL* 1.3 90.7 + - + +
155A GLN* 1.3 70.2 + - - +
156A ASP* 3.3 28.3 + - - +
169A LEU* 5.8 3.0 - - - +
170A SER 3.3 24.5 + - - -
171A TRP* 3.6 30.6 - - + +
1296B LEU* 4.9 0.7 - - - -
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Residues in contact with GLN 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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142A MET* 5.6 7.2 - - + -
143A VAL 3.1 5.2 - - - -
144A ASN* 3.1 26.0 - - - +
152A PRO* 5.8 0.9 - - + -
153A VAL 4.9 0.2 - - - +
154A LYS* 1.3 79.3 - - - +
156A ASP* 1.3 73.0 + - - +
1293B SER* 5.5 6.0 - - - -
1296B LEU* 3.1 47.1 - - + +
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Residues in contact with ASP 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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141A VAL 4.1 0.2 - - - +
142A MET* 3.6 10.6 - - - +
143A VAL* 2.9 33.4 + - + +
154A LYS* 3.3 30.4 + - - +
155A GLN* 1.3 91.1 + - - +
157A SER* 1.3 62.1 + - - +
158A LEU* 3.5 22.6 - - + +
169A LEU* 5.6 4.5 - - - +
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Residues in contact with SER 157 (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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140A THR* 3.9 16.6 - - - +
141A VAL 3.7 4.7 - - - -
142A MET* 3.6 23.2 - - - -
156A ASP* 1.3 75.7 - - - +
158A LEU* 1.3 61.5 + - - +
189A GLU* 5.3 1.9 + - - -
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Residues in contact with LEU 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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140A THR* 3.4 7.3 - - - +
141A VAL* 2.9 31.1 + - + +
143A VAL* 4.6 10.1 - - + -
156A ASP* 3.5 31.9 - - + +
157A SER* 1.3 76.6 - - - +
159A SER* 1.3 64.8 + - - +
167A LEU* 3.9 26.9 - - + -
168A PRO 5.0 1.1 - - - +
169A LEU* 3.4 48.2 - - + -
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Residues in contact with SER 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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138A GLY 5.3 0.2 - - - -
139A ARG 3.2 18.3 + - - -
140A THR* 3.9 12.0 + - - -
141A VAL 4.5 0.7 - - - +
158A LEU* 1.3 81.1 - - - +
160A SER* 1.3 58.7 + - - +
161A GLN* 3.0 29.5 + - - +
163A GLN* 4.7 1.7 - - - +
167A LEU* 3.5 13.5 - - - +
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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