Contacts of the strand formed by residues 236 - 240 (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 VAL 236 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ILE* 3.8 24.2 - - + +
9A LYS* 3.7 26.5 - - + -
55A SER* 3.4 24.9 - - - +
112A GLN* 4.7 2.9 - - + +
113A VAL 4.5 0.9 - - - -
114A ALA* 3.7 15.2 - - + +
129A PHE 3.3 13.0 - - - +
130A ALA* 4.2 5.6 - - + -
139A PHE* 4.2 1.3 - - - -
217A ASN* 3.3 3.1 - - - +
218A SER* 2.9 47.9 + - - +
234A ASP 3.9 0.2 + - - -
235A PRO* 1.3 80.3 - - - +
237A LEU* 1.3 62.3 + - - +
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Residues in contact with LEU 237 (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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7A ILE* 3.7 4.2 - - - +
114A ALA* 4.4 0.4 - - - -
127A ILE 3.7 1.4 - - - +
128A ALA* 3.5 3.6 - - - -
129A PHE* 2.8 58.8 + - + +
139A PHE* 3.7 32.1 - - + -
143A LEU* 3.9 31.0 - - + -
146A MET* 4.9 1.6 - - + -
215A ALA* 4.4 0.2 - - + -
216A ALA 3.3 26.9 - - - +
217A ASN* 3.9 11.0 - - + +
236A VAL* 1.3 77.5 - - - +
238A LEU* 1.3 68.3 + - - +
239A VAL* 3.9 13.5 - - + -
255A PHE* 4.4 9.9 - - + -
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Residues in contact with LEU 238 (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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5A VAL* 3.4 48.2 - - + +
7A ILE* 3.4 29.2 - - + -
57A LEU* 4.3 1.6 - - + -
114A ALA* 3.4 23.6 - - + +
115A GLU* 3.9 4.5 - - - +
116A MET* 3.8 19.7 - - + +
126A ILE* 4.5 10.3 - - + -
127A ILE 3.5 9.0 - - - +
128A ALA* 4.3 7.9 - - + -
215A ALA* 3.1 6.9 - - - +
216A ALA* 2.9 32.0 + - + +
237A LEU* 1.3 72.9 - - - +
239A VAL* 1.3 62.2 + - - +
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Residues in contact with VAL 239 (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* 4.7 0.2 - - - -
126A ILE* 3.4 4.6 - - - +
127A ILE* 2.9 38.6 + - + +
129A PHE* 3.9 16.2 - - + -
143A LEU* 4.7 0.2 - - + -
146A MET* 4.1 19.3 - - - -
147A PHE* 4.3 7.6 - - + -
214A ALA 3.5 8.1 - - - +
215A ALA* 4.2 6.7 - - + -
237A LEU* 3.9 22.2 - - + -
238A LEU* 1.3 80.8 - - - +
240A ARG* 1.3 77.6 + - - +
241A ALA* 4.0 0.6 + - + -
246A PRO* 5.7 0.2 - - + -
251A VAL* 3.8 28.5 - - + -
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Residues in contact with ARG 240 (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* 3.9 15.9 - - + +
118A PHE* 3.4 47.7 - - + +
119A GLU 3.6 9.3 + - - -
121A ARG* 3.3 23.1 - - - +
124A GLU* 2.9 37.7 + - - +
125A PRO 3.8 4.3 - - - -
126A ILE* 4.1 10.8 - - + -
147A PHE* 5.2 0.5 - - - -
212A ALA* 4.3 9.5 - - - +
213A PRO* 2.9 34.6 + - - +
214A ALA 2.9 12.2 + - - +
239A VAL* 1.3 85.6 - - - +
241A ALA* 1.3 59.5 + - - +
245A LEU* 3.6 30.7 - - + +
246A PRO* 4.5 3.3 - - - +
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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