Contacts of the strand formed by residues 130 - 137 (chain A) in PDB entry 2P0R
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 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A PHE* 3.8 29.0 - - + +
32A MET* 4.0 19.3 - - + -
33A ARG* 3.6 37.0 - - + +
43A PHE* 3.7 30.5 - - + -
127A TYR* 5.4 0.7 - - - -
128A ALA* 4.3 11.6 + - + +
129A GLY* 1.3 77.5 - - - +
131A PHE* 1.3 77.8 + - - +
145A VAL* 3.7 23.8 - - + -
146A ILE 3.4 11.7 - - - +
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Residues in contact with PHE 131 (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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29A PHE* 4.0 3.1 - - - -
79A PHE* 3.3 37.0 - + - -
121A GLN* 3.4 29.2 - - + -
122A SER 3.7 21.8 - - - -
123A PHE* 3.7 23.6 - + - -
127A TYR* 3.8 9.9 - + - -
130A ILE* 1.3 89.4 - - - +
132A HIS* 1.3 60.0 + - - +
133A PHE* 4.3 10.5 - - + -
145A VAL* 3.5 1.4 - - - -
146A ILE* 2.7 49.6 + - + +
148A ASP* 3.7 38.6 - - + -
172A LEU* 4.0 6.7 - - + -
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Residues in contact with HIS 132 (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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29A PHE* 3.2 57.1 - + + +
30A GLU* 5.3 1.1 - - - -
118A PRO* 3.2 43.9 - - + +
119A GLN 5.4 1.8 - - - -
121A GLN* 2.9 38.8 + - + -
131A PHE* 1.3 76.0 - - - +
133A PHE* 1.3 68.4 + - - +
134A GLN* 5.1 2.1 + - - -
143A ASP* 2.7 30.1 - - - +
144A VAL 3.2 13.2 - - - +
145A VAL* 4.0 7.0 - - + -
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Residues in contact with PHE 133 (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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79A PHE* 3.7 32.5 - + - -
116A VAL 3.2 16.2 - - - +
117A ILE* 4.0 16.6 - - + -
118A PRO* 4.0 1.3 - - - -
131A PHE* 4.3 6.7 - - + -
132A HIS* 1.3 83.0 - - - +
134A GLN* 1.3 64.5 + - - +
135A PHE* 4.0 19.5 - - + -
142A LEU 3.8 0.2 - - - +
143A ASP* 3.8 3.0 - - - +
144A VAL* 2.8 35.0 + - - +
146A ILE* 3.8 14.1 - - + -
169A TRP 4.0 2.2 - - - -
172A LEU* 3.7 22.9 - - + -
173A LEU* 3.5 39.0 - - + -
176A ALA* 3.5 19.1 - - + -
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Residues in contact with GLN 134 (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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19A ALA* 3.1 34.7 - - - +
115A ARG 3.3 22.6 + - - +
116A VAL* 2.8 39.5 + - - +
118A PRO* 4.0 21.4 - - + +
132A HIS* 5.4 1.2 + - - -
133A PHE* 1.3 75.7 - - - +
135A PHE* 1.3 61.7 + - - +
141A TRP* 3.7 15.2 - - + -
142A LEU 3.2 15.4 - - - +
143A ASP* 3.6 19.8 + - - +
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Residues in contact with PHE 135 (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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116A VAL* 4.0 5.2 - - + -
133A PHE* 4.0 6.7 - - + -
134A GLN* 1.3 78.1 - - - +
136A TRP* 1.3 63.5 + - - +
137A GLN* 3.7 1.4 + - + +
141A TRP* 3.5 6.9 - - - -
142A LEU* 2.8 34.7 + - + +
144A VAL* 3.8 26.9 - - + -
173A LEU* 3.5 32.8 - - + -
176A ALA* 3.8 31.4 - - + -
177A TYR* 3.8 34.1 - + - -
180A LEU* 3.8 27.6 - - + -
198A ASP* 3.6 5.4 - - + +
199A PHE* 4.0 17.5 - + - -
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Residues in contact with TRP 136 (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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135A PHE* 1.3 69.6 - - - +
137A GLN* 1.3 75.2 + - - +
138A HIS* 3.8 13.7 + - - -
139A SER* 3.4 28.0 - - - -
140A GLU* 3.2 27.6 - - - -
141A TRP* 3.3 47.3 - + + -
197A GLU* 3.8 14.1 - - + +
198A ASP* 2.7 35.4 + - - +
201A GLY* 3.3 38.0 + - - +
202A GLY 5.6 0.6 + - - -
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Residues in contact with GLN 137 (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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135A PHE 3.7 2.0 + - - +
136A TRP* 1.3 96.7 - - - +
138A HIS* 1.3 79.7 + - + +
139A SER 3.1 0.2 + - - -
140A GLU* 2.6 37.1 + - - +
142A LEU* 3.9 31.4 - - + +
180A LEU* 3.8 33.2 + - + +
181A ASN* 5.7 2.6 + - - -
198A ASP* 3.1 20.6 + - - +
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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