Contacts of the helix formed by residues 140 - 155 (chain C) in PDB entry 2GJD
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 140 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C SER* 2.8 13.8 + - - +
139C ARG* 1.3 83.1 - - + +
141C LYS* 1.3 63.2 + - - +
142C ALA* 3.8 10.5 - - - +
143C GLU* 3.0 55.3 + - + +
144C TYR 3.0 10.2 + - - -
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Residues in contact with LYS 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C ASN* 5.4 1.0 - - - +
136C SER 3.3 4.6 + - - -
137C PHE* 3.6 41.4 + - + +
138C SER 5.4 0.2 - - - -
139C ARG 4.0 0.2 - - - -
140C ASN* 1.3 75.0 - - - +
142C ALA* 1.3 57.6 + - - +
144C TYR* 3.2 19.8 + - + +
145C ASP* 2.8 66.4 + - - +
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Residues in contact with ALA 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C ASN* 3.2 9.3 - - - +
141C LYS* 1.3 77.9 - - - +
143C GLU* 1.3 57.1 + - - +
145C ASP* 3.6 7.7 + - - +
146C LYS* 3.0 28.1 + - - +
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Residues in contact with GLU 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C TYR* 5.3 0.9 - - - +
136C SER* 2.7 25.8 + - - +
140C ASN* 3.0 34.7 + - - +
142C ALA* 1.3 73.8 - - - +
144C TYR* 1.3 66.6 + - - +
146C LYS* 3.3 8.7 + - - +
147C LYS* 3.1 22.9 + - + +
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Residues in contact with TYR 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C TRP* 4.0 17.3 - + - -
82C TYR* 3.4 37.0 - + - -
83C HIS* 4.4 0.3 - - - -
84C PRO* 3.2 39.3 - - + +
120C LEU 4.5 0.9 + - - -
123C PRO* 3.9 9.6 - - + +
133C ALA 3.5 12.3 - - - -
136C SER* 3.8 2.6 - - - +
137C PHE* 3.6 37.0 - + + +
140C ASN 3.0 8.5 + - - +
141C LYS* 3.4 18.2 - - - +
143C GLU* 1.3 76.9 - - - +
145C ASP* 1.3 76.1 + - - +
147C LYS* 3.2 5.0 + - - +
148C VAL* 3.0 39.7 + - + +
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Residues in contact with ASP 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C ASN* 3.5 27.8 + - - +
141C LYS* 2.8 62.3 + - - +
142C ALA* 3.9 7.5 - - - +
144C TYR* 1.3 77.6 - - - +
146C LYS* 1.3 57.2 + - - +
148C VAL* 3.1 5.9 + - - +
149C LEU* 2.8 37.5 + - + +
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Residues in contact with LYS 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C ALA 3.0 19.0 + - - +
143C GLU* 3.6 8.3 - - - +
144C TYR 3.3 0.2 - - - -
145C ASP* 1.3 75.6 - - - +
147C LYS* 1.3 63.5 + - - +
149C LEU* 3.4 11.5 + - - +
150C LEU* 3.1 44.2 + - + +
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Residues in contact with LYS 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C TYR* 3.4 56.0 - - + +
143C GLU* 3.1 13.7 + - + +
144C TYR 3.6 7.9 - - - +
146C LYS* 1.3 78.5 - - - +
148C VAL* 1.3 56.5 + - - +
150C LEU* 3.3 9.3 + - + -
151C GLN* 2.9 38.4 + - - +
154C GLN* 5.6 4.1 + - - -
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Residues in contact with VAL 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C ASN* 3.7 22.0 - - + +
53C TRP* 3.4 53.1 - - + +
58C TYR* 4.8 0.5 + - - -
82C TYR* 4.4 8.5 - - + -
144C TYR* 3.0 44.9 + - + +
145C ASP* 3.6 8.5 - - - +
147C LYS* 1.3 74.7 - - - +
149C LEU* 1.3 62.9 + - - +
151C GLN* 3.2 8.6 + - - +
152C ALA* 2.9 22.9 + - - +
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Residues in contact with LEU 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C ASN* 3.6 44.0 - - + +
145C ASP* 2.8 25.8 + - + +
146C LYS* 3.7 9.4 - - - +
148C VAL* 1.3 77.5 - - - +
150C LEU* 1.3 64.2 + - + +
152C ALA* 3.3 6.2 + - + +
153C LYS* 3.2 27.5 + - - +
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Residues in contact with LEU 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C LYS* 3.1 41.4 + - + +
147C LYS* 3.8 10.5 - - + +
149C LEU* 1.3 74.2 - - + +
151C GLN* 1.3 61.3 + - - +
153C LYS* 3.2 33.8 + - + +
154C GLN* 2.9 26.2 + - - +
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Residues in contact with GLN 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C TRP* 3.5 23.6 - - - -
58C TYR* 3.9 4.0 - - + -
80C GLY 4.9 0.2 - - - +
81C PHE* 3.6 21.5 - - + -
82C TYR* 2.9 55.0 + - - +
147C LYS* 2.9 26.6 + - - +
148C VAL* 3.2 5.5 + - - +
150C LEU* 1.3 74.6 - - - +
152C ALA* 1.3 57.7 + - - +
154C GLN* 3.2 18.1 + - - +
155C TYR* 3.0 44.2 + - + +
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Residues in contact with ALA 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C ASN 3.7 14.4 - - - +
53C TRP 4.0 0.2 - - - +
54C ALA 3.7 17.7 - - - +
56C GLY* 3.6 3.6 - - - +
58C TYR* 3.3 26.8 + - - +
148C VAL 2.9 12.7 + - - +
149C LEU* 3.4 11.9 - - + +
150C LEU 3.3 0.2 - - - -
151C GLN* 1.3 74.3 - - - +
153C LYS* 1.3 57.4 + - + +
155C TYR 3.3 3.5 + - - -
156C SER* 2.8 30.8 + - - -
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Residues in contact with LYS 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C LEU* 3.2 15.5 + - - +
150C LEU* 3.5 32.6 - - + +
152C ALA* 1.3 75.3 - - + +
154C GLN* 1.3 65.7 + - - +
156C SER* 3.0 23.4 + - - +
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Residues in contact with GLN 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C LYS* 5.6 4.3 + - - -
150C LEU 2.9 12.6 + - - +
151C GLN* 3.2 22.3 - - - +
153C LYS* 1.3 77.0 - - - +
155C TYR* 1.3 98.0 + - + +
156C SER 3.6 2.3 + - - +
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Residues in contact with TYR 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C VAL* 2.8 40.8 + - - +
58C TYR* 3.7 26.7 - + + -
59C PRO* 3.4 34.1 - - + -
78C PRO* 3.4 25.5 - - + +
81C PHE* 3.8 20.8 - + - -
151C GLN* 3.0 28.8 + - + +
152C ALA 3.4 4.5 - - - -
153C LYS 3.1 0.2 - - - -
154C GLN* 1.3 112.6 + - + +
156C SER* 1.3 65.8 + - - +
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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