Contacts of the strand formed by residues 116 - 120 (chain B) in PDB entry 5WN0
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A GLU* 3.9 6.1 - - - -
118A TYR* 5.8 0.7 - - - -
119A TRP 3.1 25.8 + - - -
120A SER* 5.0 1.8 - - - -
144A TYR* 3.5 39.4 - + - -
115B SER* 1.3 76.9 + - - +
117B GLN* 1.3 59.0 + - - +
118B TYR* 3.6 25.9 - - + +
133B LEU 3.5 2.6 - - - +
134B LEU* 3.3 2.6 - - - -
135B SER 2.9 34.4 + - - +
136B ARG 3.0 25.6 + - - -
137B GLN 4.2 1.1 - - - +
138B ALA* 3.6 34.9 + - + +
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Residues in contact with GLN 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B GLU* 5.6 0.2 - - - +
108B LEU* 2.9 36.1 + - - +
109B GLN* 4.5 7.6 - - - +
111B LEU* 4.4 2.2 + - - +
114B LEU 3.1 20.9 + - - +
115B SER* 3.3 19.6 + - - +
116B HIS* 1.3 75.1 - - - +
118B TYR* 1.3 71.9 + - - +
119B TRP* 3.7 29.8 + - - +
133B LEU 3.4 4.3 - - - -
134B LEU* 3.3 23.9 - - + +
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Residues in contact with TYR 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B GLU* 5.5 0.4 - - - -
116B HIS* 3.6 33.9 - + + +
117B GLN* 1.3 79.6 - - - +
119B TRP* 1.3 63.6 + - - +
132B GLY* 3.2 1.6 - - - -
133B LEU* 2.8 57.8 + - + +
138B ALA* 4.1 6.6 - - - +
139B PRO* 3.1 38.9 + - + +
142B VAL* 3.7 28.8 - - + +
144B TYR* 3.6 21.5 - - - +
158B ILE* 3.2 14.4 - - + +
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Residues in contact with TRP 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B LEU* 3.8 28.3 - - + -
94B LEU* 4.0 26.2 - - + -
97B THR* 4.6 10.8 - - + -
101B GLU* 3.5 41.7 + - + +
104B LEU* 3.4 30.4 - - + +
108B LEU* 4.1 21.3 - - + -
117B GLN* 3.7 35.4 + - + +
118B TYR* 1.3 82.0 - - - +
120B SER* 1.3 62.1 + - - +
121B ALA 4.2 0.2 - - - -
131B VAL 3.6 7.4 - - - +
132B GLY* 3.7 18.2 - - - -
134B LEU* 4.1 13.0 - - + -
144B TYR* 3.8 13.9 + - - -
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Residues in contact with SER 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B THR* 5.0 0.5 + - - -
99B CYS 5.8 0.2 - - - -
119B TRP* 1.3 76.5 - - - +
121B ALA* 1.3 60.7 + - - +
130B GLY* 3.3 5.7 - - - -
131B VAL* 3.1 45.2 + - - +
144B TYR* 3.6 33.3 - - - +
155B GLY* 3.5 16.5 + - - +
157B VAL 4.4 2.6 + - - -
158B ILE* 4.3 2.2 - - - -
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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