Contacts of the helix formed by residues 116 - 124 (chain B) in PDB entry 2C4Y
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 116 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A PHE* 3.4 29.6 - - + +
8A VAL 4.1 6.8 + - - -
110B GLY 2.7 27.9 + - - -
111B LEU 4.2 4.5 - - - +
113B LYS* 3.1 30.5 + - - +
114B ASP 4.8 1.9 - - - +
115B GLY* 1.3 81.1 - - - +
117B PRO* 1.3 72.6 - - + +
118B ILE 3.6 0.4 - - - -
119B PRO* 3.3 10.1 - - + +
120B SER* 2.7 25.7 + - - -
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Residues in contact with PRO 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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3A ASN* 3.3 31.7 + - + +
5A THR* 3.5 29.4 - - - +
7A PHE* 3.6 26.2 - - + -
32A TRP* 3.7 20.4 - - + -
115B GLY 4.6 0.7 - - - +
116B ASN* 1.3 88.6 - - + +
118B ILE* 1.3 64.8 + - + +
120B SER* 3.1 6.4 + - - -
121B ALA* 2.9 25.6 + - - +
128B ILE* 4.9 4.0 - - + -
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Residues in contact with ILE 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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7A PHE* 5.2 5.2 - - + -
32A TRP* 4.0 19.1 - - + -
44A VAL* 5.2 3.1 - - + -
46A CYS* 3.5 38.8 - - + -
60A ILE* 3.5 33.4 - - + -
111B LEU* 3.9 28.3 - - + +
112B LEU* 5.0 7.9 - - + -
116B ASN* 4.9 0.2 - - - +
117B PRO* 1.3 76.4 - - + +
119B PRO* 1.3 71.7 - - + +
121B ALA* 3.2 4.8 + - - +
122B ILE* 3.1 37.6 + - + +
128B ILE* 4.7 2.2 - - + -
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Residues in contact with PRO 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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105A VAL* 3.7 32.3 - - + +
108A MET* 6.0 0.4 - - + -
109A GLN* 4.9 1.1 - - - +
111B LEU 3.3 16.2 - - - +
112B LEU* 3.8 17.5 - - + +
113B LYS 3.2 26.7 - - - +
114B ASP* 5.3 1.6 - - - +
115B GLY 4.8 1.6 - - - +
116B ASN 3.3 13.9 - - - +
118B ILE* 1.3 95.2 - - + +
120B SER* 1.3 54.8 + - - +
122B ILE* 3.5 4.9 + - + -
123B ALA* 3.0 32.2 + - - +
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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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3A ASN* 5.1 8.7 - - - -
115B GLY* 3.6 21.5 + - - -
116B ASN 2.7 24.7 + - - -
117B PRO* 3.5 4.9 - - - -
119B PRO* 1.3 77.7 - - - +
121B ALA* 1.3 62.8 + - - +
123B ALA* 3.7 4.9 + - - +
124B ALA* 3.3 23.4 + - - +
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Residues in contact with ALA 121 (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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3A ASN* 3.5 25.5 - - - +
58A TYR* 4.8 4.5 - - + -
117B PRO 2.9 13.6 + - - +
118B ILE* 3.7 4.9 - - - +
120B SER* 1.3 75.8 - - - +
122B ILE* 1.3 64.6 + - - +
124B ALA 3.2 5.0 + - - -
126B SER* 2.8 40.1 + - - +
127B GLY* 3.7 12.8 - - - +
128B ILE* 4.1 11.4 - - + -
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Residues in contact with ILE 122 (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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58A TYR* 3.7 31.3 + - + -
60A ILE* 4.4 10.1 - - + -
90A LEU* 3.9 31.9 - - + -
92A ILE* 4.1 13.5 - - + +
101A CYS* 3.4 18.6 - - + +
104A ILE* 5.0 2.0 - - + -
105A VAL* 3.8 14.8 - - + -
108A MET* 4.1 15.0 - - + -
112B LEU* 5.6 0.7 - - + -
118B ILE* 3.1 35.7 + - + +
119B PRO* 3.8 5.4 - - + +
121B ALA* 1.3 76.1 - - - +
123B ALA* 1.3 61.8 + - - +
124B ALA 3.2 1.4 + - - -
125B ASN* 3.2 10.7 + - - -
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Residues in contact with ALA 123 (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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98A ASN* 3.6 27.5 - - - +
101A CYS* 3.9 12.6 - - - -
102A GLU* 3.9 25.5 - - + +
105A VAL* 4.1 11.7 - - + -
119B PRO 3.0 18.2 + - - +
120B SER* 4.1 6.3 - - - +
122B ILE* 1.3 76.6 - - - +
124B ALA* 1.3 57.8 + - - +
125B ASN 3.5 0.2 - - - -
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Residues in contact with ALA 124 (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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98A ASN* 3.7 13.6 + - - +
120B SER 3.3 15.7 + - - +
121B ALA 3.2 2.5 + - - +
122B ILE 3.1 1.0 - - - -
123B ALA* 1.3 77.1 - - - +
125B ASN* 1.3 71.9 + - - +
126B SER* 3.0 18.6 + - - +
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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