Contacts of the strand formed by residues 202 - 207 (chain A) in PDB entry 4X61
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 ILE 202 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A LEU* 3.9 12.1 - - + -
142A ILE* 3.8 18.6 - - + -
150A MET* 4.5 0.4 - - - -
151A PHE* 3.6 6.3 - - + +
153A MET* 3.8 28.5 - - + -
189A TRP* 3.6 21.2 - - + -
192A PHE* 4.0 9.6 - - + -
193A ARG* 5.4 3.8 - - + -
196A CYS* 3.5 39.3 - - + -
199A SER* 3.3 31.0 + - - +
200A LYS 3.4 1.6 - - - -
201A ARG* 1.3 81.8 - - - +
203A ALA* 1.3 61.5 + - - +
225A PRO* 4.3 7.3 - - - +
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Residues in contact with ALA 203 (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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150A MET* 3.6 22.1 - - + +
151A PHE 2.8 10.4 + - - +
152A TRP* 4.3 3.4 - - + -
153A MET* 2.9 31.2 + - - +
189A TRP* 4.1 3.1 - - - -
202A ILE* 1.3 73.7 - - - +
204A VAL* 1.3 65.9 + - - +
225A PRO* 3.3 19.5 - - + +
227A LYS* 3.6 20.9 - - + -
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Residues in contact with VAL 204 (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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152A TRP* 5.1 2.5 - - - -
153A MET 3.9 2.7 - - - -
155A VAL* 3.8 16.2 - - + -
189A TRP* 3.5 46.9 - - + +
203A ALA* 1.3 73.3 - - - +
205A ALA* 1.3 62.7 + - - +
206A LEU* 3.7 23.3 - - + +
221A TRP* 4.1 17.3 - - + -
224A GLU* 5.1 0.9 - - + -
225A PRO* 2.8 20.1 + - + +
226A ILE* 3.6 14.0 - - + -
227A LYS* 3.0 24.3 + - - +
228A ALA 3.2 8.5 + - - +
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Residues in contact with ALA 205 (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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123A LEU* 3.9 27.1 - - + -
152A TRP* 4.0 9.4 - - + -
153A MET 2.9 15.4 + - - +
154A ARG* 3.4 2.7 - - - -
155A VAL 3.1 23.4 + - - -
203A ALA 4.1 0.4 + - - -
204A VAL* 1.3 72.0 - - - +
206A LEU* 1.3 61.2 + - - +
207A GLU 3.5 1.4 + - - -
228A ALA* 3.3 19.3 - - + -
230A ILE* 4.1 13.8 - - + +
265A ILE* 5.2 0.4 - - + -
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Residues in contact with LEU 206 (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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155A VAL 3.3 14.4 - - - +
157A LEU* 3.9 29.2 - - + +
204A VAL* 3.7 8.9 - - + +
205A ALA* 1.3 71.1 - - - +
207A GLU* 1.3 59.3 + - - +
208A ILE* 3.7 20.0 + - + +
221A TRP* 3.7 55.6 - - + +
226A ILE* 4.4 16.4 - - + -
228A ALA 2.9 13.6 + - - +
229A ALA* 3.4 4.9 - - + -
230A ILE 2.8 28.2 + - - -
253A LEU* 5.8 4.7 - - + -
257A LEU* 5.3 7.2 - - + -
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Residues in contact with GLU 207 (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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154A ARG* 2.9 58.1 + - + +
155A VAL 2.8 12.2 + - - +
156A PRO* 3.4 23.0 - - + +
157A LEU* 2.8 32.9 + - - +
206A LEU* 1.3 71.6 - - - +
208A ILE* 1.3 61.5 + - - +
209A GLY 3.9 0.7 + - - -
230A ILE* 3.6 21.5 - - + +
232A PRO* 4.3 12.5 - - + +
267A THR* 4.5 0.7 - - - +
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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