Contacts of the strand formed by residues 117 - 121 (chain A) in PDB entry 3WF4
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 LEU 117 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A LYS* 4.3 15.3 - - + -
48A PHE* 3.7 35.4 - - + -
78A ASN* 3.0 19.0 + - + +
79A ALA* 4.0 9.4 - - + -
80A ILE* 3.0 22.7 + - - +
112A HIS* 5.7 2.7 - - + -
115A GLY 5.1 3.1 - - - +
116A LEU* 1.3 79.2 - - - +
118A VAL* 1.3 68.4 + - - +
174A TYR* 3.9 22.9 - - + -
178A GLY 5.2 0.2 - - - +
179A PRO* 3.4 17.3 - - + +
181A ILE* 3.9 24.7 - - + -
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Residues in contact with VAL 118 (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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80A ILE* 3.4 25.4 - - + +
82A THR* 5.1 1.3 - - + -
108A LEU* 3.8 25.1 - - + -
111A ALA* 3.8 20.2 - - + -
117A LEU* 1.3 82.0 - - - +
119A ILE* 1.3 77.8 + - - +
120A LEU* 4.0 7.4 - - + +
179A PRO* 2.7 31.8 + - + +
180A VAL* 3.2 13.4 - - + +
181A ILE* 3.0 28.8 + - - +
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Residues in contact with ILE 119 (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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50A TYR* 3.7 44.2 - - + +
52A SER* 4.0 9.9 - - - +
79A ALA* 3.9 20.2 - - + -
80A ILE 2.9 10.9 + - - +
81A GLN* 3.3 27.4 - - + +
82A THR 3.3 23.6 + - - -
118A VAL* 1.3 77.2 - - - +
120A LEU* 1.3 60.0 + - - +
121A ARG* 4.4 2.7 - - + -
181A ILE* 4.4 6.3 - - + -
182A THR* 3.1 28.5 - - - +
218A PHE* 3.8 20.6 - - + -
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Residues in contact with LEU 120 (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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82A THR* 4.1 16.8 - - + -
84A VAL* 3.8 23.8 - - + -
104A VAL* 5.0 1.1 - - + -
108A LEU* 4.2 21.8 - - + -
118A VAL* 3.9 3.7 - - + -
119A ILE* 1.3 71.8 - - - +
121A ARG* 1.3 62.7 + - - +
122A PRO* 3.3 21.8 - - + +
166A LEU* 5.6 1.8 - - + -
169A MET* 3.6 35.4 - - + -
180A VAL* 4.1 20.4 - - + -
182A THR 3.0 9.4 + - - +
183A VAL* 3.3 13.9 - - + -
184A GLN 2.9 24.3 + - - -
211A LEU* 6.5 0.9 - - + -
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Residues in contact with ARG 121 (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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81A GLN* 3.1 36.8 - - + +
82A THR 2.9 16.7 + - - +
83A TYR* 2.8 54.2 + - + -
84A VAL 3.0 20.5 + - - -
119A ILE* 4.2 2.9 - - + +
120A LEU* 1.3 79.8 - - - +
122A PRO* 1.4 57.9 - - - +
123A GLY 3.3 8.2 + - - +
126A ILE* 3.9 0.3 - - - +
184A GLN* 3.0 43.2 + - + +
187A ASN* 3.6 4.4 + - - -
218A PHE* 4.5 3.4 - - - -
220A THR* 4.4 4.2 + - - -
267A SER* 4.6 0.8 + - - -
268A GLU* 2.8 29.5 + - - +
306A TYR* 3.5 7.9 - - - -
705A CL 3.1 23.2 - - - +
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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