Contacts of the strand formed by residues 116 - 120 (chain A) in PDB entry 5WN1
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 HIS 116 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A SER* 1.3 91.7 + - - +
117A GLN* 1.3 58.8 + - - +
118A TYR* 3.5 25.9 - - - +
134A LEU* 3.2 3.8 - - - -
135A SER* 2.9 44.6 + - - +
136A ARG 3.4 19.9 + - - -
137A GLN* 4.4 0.9 - - - +
138A ALA* 3.6 37.8 + - + +
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Residues in contact with GLN 117 (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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104A LEU* 5.7 0.5 - - - +
108A LEU* 2.9 35.9 + - - +
111A LEU* 4.6 4.9 + - - +
114A LEU 3.3 21.3 + - - +
115A SER* 3.7 10.3 + - - +
116A HIS* 1.3 77.7 - - - +
118A TYR* 1.3 71.9 + - - +
119A TRP* 3.7 28.7 + - - +
133A LEU 3.6 3.6 - - - -
134A LEU* 3.6 27.8 - - + +
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Residues in contact with TYR 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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116A HIS* 3.5 41.2 - - + +
117A GLN* 1.3 78.4 - - - +
119A TRP* 1.3 66.9 + - - +
132A GLY* 3.5 3.3 - - - -
133A LEU* 3.1 49.5 + - + +
135A SER* 4.1 2.5 - - - -
138A ALA* 4.4 2.6 - - - +
139A PRO* 3.4 33.6 + - + +
142A VAL* 3.8 28.2 - - + +
144A TYR* 3.6 23.1 - - + +
158A ILE* 3.5 11.3 - - + +
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Residues in contact with TRP 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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72A LEU* 3.9 18.4 - - + -
94A LEU* 4.3 10.3 - - + -
97A THR* 4.4 9.6 - - + -
101A GLU* 3.8 31.6 + - + +
104A LEU* 3.4 31.1 - - + +
108A LEU* 3.7 32.8 - - + -
117A GLN* 3.7 32.9 + - + +
118A TYR* 1.3 83.1 - - - +
120A SER* 1.3 60.5 + - - +
121A ALA* 4.2 1.3 - - + +
131A VAL 3.7 8.1 - - - -
132A GLY* 3.6 25.8 - - - -
134A LEU* 3.9 24.5 - - + -
144A TYR* 3.6 19.2 + - - -
158A ILE* 4.2 0.7 - - - -
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Residues in contact with SER 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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97A THR* 5.0 1.0 - - - +
119A TRP* 1.3 75.1 - - - +
121A ALA* 1.3 61.1 + - - +
130A GLY* 3.3 5.9 - - - -
131A VAL* 3.2 32.9 + - - -
144A TYR* 3.9 26.1 - - - +
155A GLY* 3.4 21.7 - - - +
156A ARG 4.6 0.2 + - - -
157A VAL 4.3 6.1 + - - -
158A ILE* 4.0 13.0 - - - +
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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