Contacts of the strand formed by residues 125 - 130 (chain H) in PDB entry 2I2X
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 THR 125 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122H THR* 4.9 2.4 + - - -
124H GLY* 1.3 73.9 - - - -
126H VAL* 1.3 81.8 + - - +
153H ASN* 3.3 37.5 + - - +
155H VAL* 4.5 10.3 - - + +
173H GLU* 4.3 35.5 + - + +
174H LYS 5.3 0.4 + - - -
175H PRO* 3.9 6.2 - - + +
176H ILE* 3.1 27.5 + - - +
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Residues in contact with VAL 126 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125H THR* 1.3 82.4 - - - +
127H VAL* 1.3 63.2 + - - +
128H CYS* 3.8 3.0 + - - -
147H LEU* 3.7 34.1 - - + -
152H TYR* 4.0 23.6 - - + -
153H ASN 2.8 14.4 + - - +
154H VAL* 3.6 5.8 - - + +
155H VAL* 3.0 25.6 + - - +
175H PRO* 4.1 0.4 - - - -
176H ILE* 4.4 8.1 - - + -
177H MET* 3.2 33.2 - - + +
179H THR* 3.9 16.4 - - + -
238H ALA* 4.8 2.7 - - + -
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Residues in contact with VAL 127 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126H VAL* 1.3 72.0 - - - +
128H CYS* 1.3 58.5 + - - +
129H HIS* 5.5 0.9 - - + -
155H VAL* 3.4 20.2 - - + -
157H LEU* 3.4 26.5 - - + -
166H VAL* 5.0 4.7 - - + -
169H ALA* 4.1 20.0 - - + +
170H VAL* 4.4 7.6 - - + -
173H GLU* 4.6 2.5 - - + -
175H PRO* 3.5 27.6 - - + +
177H MET 3.0 7.3 + - - -
178H LEU* 3.3 26.1 - - + +
179H THR* 2.7 32.2 + - - -
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Residues in contact with CYS 128 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126H VAL* 4.3 7.4 - - - -
127H VAL* 1.3 75.6 - - - +
129H HIS* 1.3 63.5 + - - +
140H LYS* 4.6 7.0 - - + -
143H VAL* 4.3 13.5 - - - -
144H THR* 4.3 15.7 - - - +
147H LEU* 4.4 4.5 - - - -
154H VAL* 4.0 21.3 - - + -
155H VAL 3.0 13.2 + - - +
156H ASP* 4.2 4.7 - - - +
157H LEU* 3.1 30.4 + - - +
179H THR* 3.0 32.8 - - - +
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Residues in contact with HIS 129 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127H VAL* 5.5 0.2 - - + -
128H CYS* 1.3 76.8 - - - +
130H VAL* 1.3 80.1 + - - +
131H ALA* 4.1 13.0 - - - +
140H LYS* 4.6 6.1 - - - +
157H LEU* 4.0 10.1 - - + -
158H GLY 4.6 2.9 - - - -
161H VAL* 4.0 22.2 + - + -
166H VAL* 3.7 24.2 - - + -
178H LEU* 4.4 6.8 - - + +
179H THR* 2.8 26.9 + - - -
180H GLY* 3.2 23.1 - - - -
181H THR* 3.1 23.7 + - - -
190H ALA* 5.0 1.8 + - - +
191H PHE* 4.8 2.4 - + - -
194H VAL* 4.1 18.1 - - + +
207H PHE* 3.5 22.4 - + - -
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Residues in contact with VAL 130 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129H HIS* 1.3 85.8 - - - +
131H ALA* 1.3 72.6 + - - +
132H GLU 3.7 0.2 + - - -
134H ASP* 3.6 27.4 - - + +
135H VAL 4.9 0.2 - - - -
136H HIS* 3.8 25.8 - - + +
137H ASP* 4.6 1.1 - - - +
140H LYS* 3.7 38.6 - - + +
158H GLY 3.8 8.9 + - - +
159H ARG* 2.7 31.0 - - + +
161H VAL* 3.6 4.2 + - - +
181H THR* 3.6 14.4 - - - +
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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