Contacts of the helix formed by residues 108 - 116 (chain B) in PDB entry 5H8N
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 ASN 108 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B ASP* 3.8 10.1 - - - +
92B LYS* 4.6 1.5 - - + +
94B GLY* 3.5 15.6 + - - -
95B THR* 3.0 45.0 + - - -
97B GLU* 3.6 12.7 - - - +
106B GLU 4.7 1.0 + - - -
107B TRP* 1.3 74.6 - - - +
109B GLY* 1.3 64.0 + - - +
111B MET* 3.5 2.8 - - - +
112B GLY* 2.9 19.7 + - - -
179B GLN* 3.1 37.6 - - - +
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Residues in contact with GLY 109 (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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88B VAL* 3.5 7.1 - - - +
90B ASP* 2.9 29.2 + - - +
92B LYS* 3.1 22.7 - - - -
93B PHE 4.0 2.2 - - - -
94B GLY* 4.1 0.4 - - - -
108B ASN* 1.3 74.5 + - - +
110B MET* 1.3 60.8 + - - -
112B GLY* 3.2 2.3 + - - -
113B GLU* 3.1 23.6 + - - +
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Residues in contact with MET 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B VAL* 3.9 16.6 - - + +
11B THR* 3.7 29.6 - - - +
12B ILE* 3.7 15.9 - - + -
88B VAL* 3.7 17.5 - - + -
92B LYS 3.6 7.4 - - - +
93B PHE* 3.1 47.4 + - + +
109B GLY* 1.3 68.4 - - - -
111B MET* 1.3 54.7 + - - +
113B GLU* 3.7 3.0 - - - +
114B LEU* 2.8 35.9 + - - +
122B ILE* 3.6 27.9 - - + +
124B ALA* 3.7 12.3 - - + -
126B LEU* 4.1 9.6 - - + -
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Residues in contact with MET 111 (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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93B PHE 3.6 10.3 + - - +
94B GLY* 4.0 5.2 - - - -
107B TRP* 3.5 49.4 - - + -
108B ASN 3.5 9.6 - - - +
110B MET* 1.3 77.6 - - - +
112B GLY* 1.3 56.6 + - - +
114B LEU* 3.9 2.0 - - - +
115B LEU* 3.0 45.3 + - + +
122B ILE* 4.0 8.9 - - - +
126B LEU* 4.7 4.7 - - + -
132B ARG* 3.7 33.9 - - + +
135B TYR* 4.5 0.4 - - + -
136B ILE* 3.7 43.7 - - + -
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Residues in contact with GLY 112 (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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107B TRP* 3.9 23.5 - - - +
108B ASN 2.9 16.3 + - - -
109B GLY 3.2 4.0 + - - -
111B MET* 1.3 75.5 - - - +
113B GLU* 1.3 56.3 + - - +
115B LEU* 3.5 2.6 + - - +
116B SER* 2.9 35.3 + - - -
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Residues in contact with GLU 113 (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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10B VAL* 3.2 9.7 - - + +
86B HIS* 2.7 33.3 + - - -
88B VAL* 4.1 7.8 - - + +
89B ALA* 3.1 36.0 + - - +
90B ASP 4.9 0.3 + - - -
109B GLY 3.1 12.3 + - - +
110B MET* 3.3 9.6 + - - +
112B GLY* 1.3 75.1 - - - +
114B LEU* 1.4 57.8 + - - +
116B SER* 3.5 5.7 + - - -
117B GLY 3.4 2.3 + - - -
118B GLN* 2.9 58.1 + - + +
119B ALA* 3.0 12.7 + - + -
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Residues in contact with LEU 114 (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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110B MET 2.8 17.3 + - - +
111B MET 3.9 4.3 - - - +
113B GLU* 1.4 74.7 - - - +
115B LEU* 1.3 61.1 + - - +
117B GLY 3.3 2.3 + - - -
119B ALA* 3.7 12.0 - - + +
120B ASP 3.5 35.2 - - - +
121B MET* 3.8 6.7 - - - +
122B ILE* 3.7 24.5 - - + -
136B ILE* 3.8 20.2 - - + -
254B GLY 3.7 10.3 - - - +
255B MET 3.7 20.2 - - - +
256B ARG* 2.7 47.3 + - + +
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Residues in contact with LEU 115 (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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107B TRP* 3.6 34.5 - - + +
111B MET* 3.0 28.1 + - + +
112B GLY* 4.1 3.4 - - - +
114B LEU* 1.3 76.9 - - - +
116B SER* 1.3 59.2 + - - +
117B GLY 3.3 1.5 + - - -
135B TYR* 3.6 44.4 - - + +
136B ILE* 3.9 11.4 - - + -
256B ARG* 4.7 15.7 - - + +
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Residues in contact with SER 116 (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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112B GLY 2.9 21.4 + - - -
113B GLU* 3.5 6.6 + - - -
114B LEU 3.4 0.2 - - - -
115B LEU* 1.3 74.0 - - - +
117B GLY* 1.3 58.3 + - - +
118B GLN* 3.0 29.6 + - - +
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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