Contacts of the strand formed by residues 171 - 177 (chain A) in PDB entry 2R5T
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 LYS 171 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A LYS* 4.4 18.4 - - - +
128A VAL* 3.8 17.8 - - + +
129A LEU 3.3 10.3 - - - +
130A GLN* 4.5 22.9 - - + +
131A LYS* 4.4 1.3 - - - +
167A GLN* 3.3 5.0 - - - +
168A THR* 2.8 41.8 + - - +
169A ALA 3.9 0.4 - - - -
170A ASP* 1.3 92.2 - - + +
172A LEU* 1.3 63.8 + - - +
173A TYR* 3.7 27.0 + - + +
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Residues in contact with LEU 172 (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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83A ILE* 4.4 11.4 - - + -
85A LEU* 4.1 15.9 - - + -
127A LYS 3.6 0.9 - - - +
128A VAL* 3.4 5.2 - - - +
129A LEU* 2.6 55.4 + - + +
131A LYS* 5.1 7.0 - - + -
134A ILE* 3.7 27.8 - - + -
150A LEU* 3.7 18.8 - - + -
166A PHE 3.6 3.8 - - - +
167A GLN* 3.7 30.5 - - + +
171A LYS* 1.3 74.8 - - - +
173A TYR* 1.3 63.3 + - - +
174A PHE* 3.9 21.2 - - + -
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Residues in contact with TYR 173 (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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95A PRO* 3.5 31.1 - - + +
100A PHE* 4.0 20.5 - + - -
126A VAL* 3.9 13.2 - - + -
127A LYS 3.4 3.6 - - - -
128A VAL* 3.9 32.5 - - + -
165A SER* 3.2 6.8 - - - -
166A PHE* 2.7 79.4 + + + +
168A THR* 3.9 11.1 + - + +
171A LYS* 3.7 37.6 + - + +
172A LEU* 1.3 75.8 - - - +
174A PHE* 1.3 63.3 + - - +
175A VAL 4.1 0.4 - - - -
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Residues in contact with PHE 174 (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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85A LEU* 4.2 14.8 - - + -
125A ALA 3.7 0.5 - - - +
126A VAL* 3.4 4.9 - - - +
127A LYS* 2.9 49.7 + - + +
129A LEU* 4.4 11.2 - - + -
150A LEU* 5.1 0.4 - - + -
151A LEU* 3.8 22.0 - - + -
162A LEU* 4.1 5.8 - - + -
164A PHE 4.0 2.7 - - - -
165A SER* 3.8 17.7 - - - -
172A LEU* 3.9 37.5 - - + -
173A TYR* 1.3 73.5 - - - +
175A VAL* 1.3 62.8 + - - +
176A LEU* 3.7 4.8 + - + +
241A PHE* 3.5 38.6 - + + -
243A LEU* 3.7 31.2 - - + -
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Residues in contact with VAL 175 (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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98A PHE* 3.7 16.4 - - + -
124A TYR* 3.5 42.6 - - + -
125A ALA 3.9 2.0 - - - -
126A VAL* 4.5 7.9 - - + -
162A LEU* 3.7 3.2 - - - +
163A HIS* 2.8 33.2 + - + +
164A PHE* 2.9 43.1 + - + +
166A PHE* 3.7 30.5 - - + -
174A PHE* 1.3 71.9 - - - +
176A LEU* 1.3 56.2 + - - +
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Residues in contact with LEU 176 (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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112A VAL* 5.3 2.0 - - + -
124A TYR* 3.4 10.6 - - - +
125A ALA* 2.8 33.6 + - + +
127A LYS* 4.2 13.5 - - + +
160A VAL* 4.3 5.8 - - + -
161A GLY 3.3 14.8 - - - +
162A LEU* 3.8 20.4 - - + -
163A HIS* 3.8 5.6 - - - -
174A PHE 3.7 10.5 - - - +
175A VAL* 1.3 75.6 - - - +
177A ASP* 1.3 71.3 + - - +
178A TYR 3.4 0.7 + - - -
239A THR 5.5 0.2 - - - +
241A PHE* 3.6 52.7 - - + -
500A ANP 4.0 23.8 - - - +
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Residues in contact with ASP 177 (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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124A TYR* 5.0 1.6 - - - -
125A ALA* 3.7 0.5 - - - +
160A VAL* 3.7 6.8 - - + +
161A GLY* 3.0 30.4 + - - -
163A HIS* 2.7 33.3 + - - -
176A LEU* 1.3 70.5 - - - +
178A TYR* 1.3 60.7 + - - +
179A ILE* 3.4 22.4 + - + +
500A ANP 2.8 27.7 + - - -
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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