Contacts of the strand formed by residues 114 - 117 (chain B) in PDB entry 2X7N
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 114 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B CYS* 3.4 3.3 - - - +
111B ASN* 2.7 42.3 + - - +
113B TYR* 1.3 88.6 - - + +
115B ALA* 1.3 74.9 + - - +
116B LEU* 4.8 0.4 - - + -
135B VAL* 3.6 2.9 - - - -
136B GLU* 3.4 24.0 - - + +
138B PHE* 3.6 24.0 - - + -
154B LEU* 4.6 1.7 - - - +
176B LEU* 3.6 18.6 - - + +
177B LEU* 3.5 37.2 - - + +
178B GLN* 5.4 4.3 - - + +
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Residues in contact with ALA 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ILE* 4.6 10.3 - - + -
109B CYS 3.1 6.5 - - - +
110B CYS* 3.5 18.2 - - + -
114B VAL* 1.3 76.4 - - - +
116B LEU* 1.3 67.3 + - - +
117B VAL* 5.4 0.2 - - + -
129B ILE* 4.9 2.2 - - + -
133B LEU* 4.7 5.4 - - + -
135B VAL* 3.4 18.2 - - + -
136B GLU 2.9 7.6 + - - +
137B VAL* 3.3 12.0 - - + +
138B PHE 2.9 25.1 + - - -
177B LEU* 5.3 0.2 - - - -
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Residues in contact with LEU 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ILE* 3.5 3.6 - - - +
109B CYS* 2.7 43.4 + - + +
114B VAL* 4.8 0.7 - - + -
115B ALA* 1.3 77.0 - - - +
117B VAL* 1.3 63.0 + - - +
138B PHE* 3.2 13.5 - - + +
140B GLN* 4.0 14.6 - - + -
142B ILE* 3.8 28.0 - - + -
148B VAL* 3.3 15.4 - - + +
152B CYS* 5.1 1.6 - - - -
173B LEU* 4.3 13.9 - - + -
176B LEU* 3.9 28.5 - - + -
177B LEU* 3.9 30.7 - - + -
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Residues in contact with VAL 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B VAL 3.3 4.7 - - - -
108B ILE* 4.0 13.0 - - + -
115B ALA* 5.1 1.1 - - + +
116B LEU* 1.3 79.5 - - - +
118B HIS* 1.3 69.4 + - - +
119B PRO 3.1 2.6 - - - -
121B ILE* 3.9 17.0 - - + -
126B GLU* 4.1 1.6 - - - +
129B ILE* 3.6 33.0 - - + -
137B VAL* 3.4 29.8 - - + -
138B PHE 2.9 9.1 + - - +
139B ARG* 3.4 21.7 - - + -
140B GLN 3.1 21.3 + - - +
148B VAL* 4.1 4.3 - - - -
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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