Contacts of the strand formed by residues 213 - 217 (chain A) in PDB entry 3T2D
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 PRO 213 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116A MET* 3.7 23.8 - - + -
117A GLU 3.6 23.8 - - - +
118A PHE* 4.2 4.9 - - + -
205A VAL 4.0 0.4 - - - +
206A PHE* 3.7 23.1 - - + -
211A GLY 3.4 4.9 - - - +
212A ALA* 1.3 85.1 - - + +
214A ALA* 1.3 60.0 + - - +
215A ALA 5.8 0.2 - - - +
240A ARG* 2.9 40.0 + - - +
245A LEU* 4.6 1.9 - - - +
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Residues in contact with ALA 214 (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 MET* 3.8 4.7 - - - +
147A PHE* 3.7 26.7 - - + -
166A PHE* 4.4 4.7 - - + -
205A VAL* 2.9 19.6 + - + +
206A PHE* 4.4 0.9 - - - -
212A ALA 3.3 4.2 + - - +
213A PRO* 1.3 73.5 - - - +
215A ALA* 1.3 61.6 + - - +
239A VAL* 3.5 3.1 - - - +
240A ARG* 2.9 31.7 + - - +
245A LEU* 3.9 21.3 - - + -
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Residues in contact with ALA 215 (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 MET* 3.5 7.5 - - - +
143A LEU* 3.9 17.0 - - + -
147A PHE* 3.8 24.7 - - + -
204A LYS* 3.3 7.4 - - - +
205A VAL* 3.0 31.1 + - + +
213A PRO* 5.8 0.2 - - - +
214A ALA* 1.3 80.9 - - - +
216A ALA* 1.3 62.7 + - - +
237A LEU* 4.4 1.3 - - + -
238A LEU 3.1 13.0 - - - +
239A VAL* 4.2 5.4 - - + -
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Residues in contact with ALA 216 (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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114A ALA* 3.4 8.9 - - + +
115A GLU 3.4 36.6 - - - +
116A MET* 3.6 13.2 - - + -
203A ARG 3.5 6.1 - - - +
204A LYS* 3.9 11.2 - - + +
215A ALA* 1.3 75.1 - - - +
217A ASN* 1.3 60.9 + - - +
237A LEU* 3.3 3.3 - - - +
238A LEU* 2.9 32.9 + - + +
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Residues in contact with ASN 217 (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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113A VAL 4.5 1.8 - - - +
114A ALA* 4.2 3.8 - - - -
136A PRO* 3.3 22.4 + - - +
139A PHE* 3.4 29.4 - - - +
140A ASN* 4.9 1.4 + - - -
143A LEU* 4.2 7.5 - - + +
201A ILE* 3.7 10.5 - - - +
202A ILE 3.0 27.9 + - - +
203A ARG* 2.8 23.9 + - - +
216A ALA* 1.3 74.0 - - - +
218A SER* 1.3 71.1 + - - +
219A VAL* 3.3 3.9 + - - -
235A PRO* 3.9 6.8 - - - +
236A VAL 3.3 10.2 - - - +
237A LEU* 3.9 8.7 - - + -
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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