Contacts of the strand formed by residues 162 - 166 (chain A) in PDB entry 3DGG
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 VAL 162 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151A TRP* 3.7 24.2 - - + +
158A ARG 4.6 2.0 - - - +
159A GLN* 3.6 26.5 + - - +
160A ASN 3.3 1.1 - - - +
161A GLY* 1.3 77.4 - - - +
163A LEU* 1.3 70.6 + - - +
164A ASN* 3.7 25.7 - - - +
180A SER* 3.8 10.3 - - - +
181A THR 3.3 2.9 - - - +
182A LEU* 3.6 24.9 - - + -
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Residues in contact with LEU 163 (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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161A GLY 5.1 3.6 - - - +
162A VAL* 1.3 81.4 - - - +
164A ASN* 1.3 64.6 + - - +
179A SER* 3.9 1.2 + - - +
180A SER* 3.5 1.0 - - - -
181A THR* 2.8 48.3 + - - +
183A THR* 5.6 6.3 - - - +
149B LYS* 5.9 3.8 - - - +
175B VAL* 4.0 34.1 - - + +
176B LEU 5.5 0.2 - - - +
177B GLN* 3.8 41.5 - - + +
182B THR* 5.1 17.7 - - + +
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Residues in contact with ASN 164 (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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149A VAL* 5.1 7.5 + - - +
162A VAL* 3.7 12.2 - - - +
163A LEU* 1.3 76.6 - - - +
165A SER* 1.3 62.0 + - - +
166A TRP* 3.4 35.4 - - + -
178A MET* 3.4 22.1 - - + +
179A SER 3.3 2.7 - - - -
180A SER* 2.5 30.4 + - - -
175B VAL* 3.6 16.2 - - - +
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Residues in contact with SER 165 (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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164A ASN* 1.3 77.5 - - - +
166A TRP* 1.3 66.1 + - - +
178A MET* 3.3 4.6 - - - +
179A SER* 2.9 44.8 + - - -
172B PHE* 3.7 8.2 - - - -
173B PRO* 2.6 46.0 + - - +
175B VAL* 3.9 9.6 - - - +
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Residues in contact with TRP 166 (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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142A PHE* 5.1 3.4 - + - -
145A LYS 5.2 4.5 - - - -
147A ILE* 4.3 13.7 + - + +
164A ASN* 3.4 33.9 - - + -
165A SER* 1.3 78.3 + - - +
167A THR* 1.3 66.4 + - - +
168A ASP* 4.2 0.7 + - - +
177A SER 3.6 6.1 - - - +
178A MET* 3.2 51.0 - - + +
172B PHE* 4.7 0.2 - - - -
173B PRO* 3.2 23.0 - - - +
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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