Contacts of the strand formed by residues 170 - 176 (chain A) in PDB entry 1P4A
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 170 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169A SER* 1.3 82.9 + - - +
171A VAL* 1.3 67.7 + - - +
172A SER* 3.8 7.1 + - - +
187A SER* 3.9 17.0 - - - +
188A LEU* 3.4 29.6 - - - +
189A ALA* 3.7 9.1 - - + +
190A LYS* 4.5 0.4 - - - +
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Residues in contact with VAL 171 (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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170A THR* 1.3 74.9 - - - +
172A SER* 1.3 64.9 + - - +
187A SER* 3.1 4.5 - - - -
188A LEU 2.8 38.7 + - - +
190A LYS* 3.9 25.6 - - + -
218A LEU* 3.6 18.6 - - + +
221A GLU* 3.5 38.6 - - + +
222A PHE* 3.9 24.5 - - + -
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Residues in contact with SER 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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170A THR* 3.8 8.0 + - - +
171A VAL* 1.3 76.9 - - - +
173A ILE* 1.3 66.5 + - - +
185A THR* 3.9 17.8 - - - +
186A MET 3.4 4.0 - - - -
187A SER* 3.3 18.5 - - - -
221A GLU* 5.5 2.6 - - - +
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Residues in contact with ILE 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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171A VAL* 5.2 1.1 - - + -
172A SER* 1.3 74.6 - - - +
174A ASN* 1.3 82.0 + - - +
175A TYR* 4.3 0.4 - - + -
185A THR* 3.5 3.1 - - - -
186A MET* 3.1 44.2 + - + +
214A GLY* 3.2 31.6 - - - +
217A ASN* 4.0 17.0 - - + +
218A LEU* 3.1 43.1 - - + +
221A GLU* 5.5 4.0 - - + -
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Residues in contact with ASN 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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173A ILE* 1.3 85.8 - - - +
175A TYR* 1.3 65.2 + - - +
183A ILE* 4.3 23.5 - - + +
184A GLN 3.4 5.8 - - - +
185A THR* 2.7 28.9 + - - +
217A ASN* 5.1 3.8 - - - +
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Residues in contact with TYR 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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137A VAL* 5.0 1.7 - - - +
161A LYS* 3.9 23.7 - - - +
174A ASN* 1.3 77.5 - - - +
176A VAL* 1.3 75.4 + - - +
177A SER* 4.2 6.5 - - - -
183A ILE* 3.5 5.5 - - - +
184A GLN* 2.8 71.0 + - + +
185A THR 3.7 16.1 + - - -
186A MET* 3.7 34.9 - - + +
210A GLY 3.7 22.4 - - - +
211A THR* 3.8 22.6 + - + +
214A GLY* 4.1 10.5 - - - -
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Residues in contact with VAL 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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175A TYR* 1.3 85.9 - - - +
177A SER* 1.3 65.0 + - - +
181A ASN 6.1 0.2 - - - -
182A ARG 3.8 10.1 - - - +
183A ILE* 3.8 28.9 - - + +
184A GLN 4.7 0.2 - - - +
210A GLY* 3.4 28.0 + - - -
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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