Contacts of the strand formed by residues 131 - 136 (chain X) in PDB entry 1H4A
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 TRP 131 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88X HIS* 3.5 21.6 - - + -
89X ARG 3.6 15.8 + - - +
90X ILE* 3.5 28.9 - - + +
105X PHE 3.7 13.5 - - - -
106X THR 4.0 2.9 - - - -
107X GLU 3.6 21.8 - - - -
126X VAL* 3.9 11.9 - - + -
128X GLU 3.3 17.8 + - - -
129X GLY 3.6 9.9 - - - -
130X SER* 1.3 78.7 - - - +
132X VAL* 1.3 62.2 + - - +
133X LEU 4.1 0.2 - - - -
145X LEU* 3.6 6.6 - - - +
146X LEU* 2.8 42.6 + - + +
167X LEU* 3.4 37.9 - - + -
168X ARG 3.2 19.7 - - - +
169X ARG* 3.5 23.6 - - + -
170X VAL* 3.9 2.5 - - - -
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Residues in contact with VAL 132 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43X MET* 4.1 13.2 - - + -
56X PHE* 3.9 33.9 - - + -
131X TRP* 1.3 77.9 - - - +
133X LEU* 1.3 69.7 + - - +
134X TYR* 3.5 36.2 - - + +
143X GLN* 4.0 20.2 - - + +
144X TYR 3.5 7.2 - - - +
145X LEU* 4.5 1.8 - - + -
167X LEU* 3.6 3.7 - - - +
168X ARG* 2.8 37.3 + - + +
170X VAL* 3.9 9.9 - - + -
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Residues in contact with LEU 133 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92X LEU* 5.1 7.6 - - + -
121X ILE* 5.8 0.7 - - + -
124X LEU* 4.0 18.6 - - + -
131X TRP 4.1 0.6 - - - -
132X VAL* 1.3 74.0 - - - +
134X TYR* 1.3 60.7 + - - +
143X GLN* 3.5 3.1 - - - -
144X TYR* 2.9 46.8 + - + +
146X LEU* 3.8 13.4 - - + +
157X TRP* 3.5 39.0 - - + +
164X VAL* 3.2 46.2 - - + -
166X SER 3.8 6.7 - - - +
167X LEU* 4.1 16.6 - - + -
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Residues in contact with TYR 134 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56X PHE* 3.9 8.1 - - - -
69X MET* 4.4 3.8 - - + +
132X VAL* 3.5 37.3 - - + +
133X LEU* 1.3 75.5 - - - +
135X GLU* 1.3 59.3 + - - +
136X LEU 3.3 0.6 + - - +
139X TYR* 3.3 58.1 - + + -
140X ARG 3.5 12.8 - - - +
142X ARG 3.5 3.4 - - - -
143X GLN* 3.6 36.2 + - + -
144X TYR* 4.9 1.3 - - - -
164X VAL* 3.6 4.9 - - - +
165X GLY 2.9 23.4 + - - -
166X SER* 2.9 28.2 + - - +
168X ARG* 3.1 31.8 + - + -
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Residues in contact with GLU 135 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134X TYR* 1.3 71.4 - - - +
136X LEU* 1.3 75.9 + - + +
140X ARG 3.7 0.4 + - - -
141X GLY* 3.6 6.1 - - - -
142X ARG* 2.9 54.3 + - + +
144X TYR* 4.4 8.8 - - - +
161X ASN* 5.3 6.6 + - - +
163X ARG* 3.8 40.4 + - + +
164X VAL* 3.4 6.1 - - - -
165X GLY* 3.1 13.2 + - - -
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Residues in contact with LEU 136 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134X TYR* 3.6 2.1 - - - +
135X GLU* 1.3 99.1 - - + +
137X SER* 1.3 57.9 + - - +
140X ARG* 3.1 49.1 + - + +
141X GLY* 3.9 22.2 - - - +
163X ARG* 5.4 7.9 - - + +
165X GLY* 3.7 5.8 - - - -
166X SER* 2.7 25.3 + - - -
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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