Contacts of the strand formed by residues 96 - 101 (chain G) in PDB entry 1GZ0
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 PHE 96 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95G PRO* 1.3 70.9 - - - +
97G LEU* 1.3 64.6 + - - +
119G ALA* 3.3 26.0 - - + -
120G GLY 3.4 19.1 - - - +
121G VAL* 3.3 21.0 - - + +
122G HIS* 2.9 45.4 + + + +
191G LEU* 3.5 14.8 - - + -
193G LEU* 5.5 2.5 - - + -
235G LEU* 3.9 31.9 - - + -
238G ALA* 4.0 18.6 - - + -
239G VAL* 4.2 7.6 - - + -
242G ARG* 3.3 34.3 - - - +
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Residues in contact with LEU 97 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85G LEU* 6.2 0.4 - - + -
89G ILE* 4.8 8.5 - - + -
92G LEU* 4.4 13.2 - - + -
95G PRO* 3.8 13.9 - - + -
96G PHE* 1.3 93.9 - - - +
98G LEU* 1.3 62.3 + - - +
99G ILE* 5.2 1.8 - - + -
121G VAL* 4.2 1.8 - - - -
122G HIS* 4.7 4.0 - - + -
123G ALA* 3.5 18.8 - - + +
125G ILE* 4.4 14.8 - - + -
164G LEU* 3.7 38.1 - - + -
169G ILE* 4.0 11.0 - - + -
191G LEU 3.0 13.6 + - - +
192G ALA* 3.4 8.4 - - + -
193G LEU* 2.9 27.8 + - - +
235G LEU* 5.7 0.2 - - - +
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Residues in contact with LEU 98 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97G LEU* 1.3 73.4 - - - +
99G ILE* 1.3 61.1 + - - +
100G LEU* 4.0 18.6 - - + -
112G CYS* 4.2 7.9 - - + +
116G ALA* 3.9 23.6 - - + -
121G VAL* 3.8 18.5 - - + +
123G ALA 2.9 7.5 + - - +
124G VAL* 3.1 16.5 - - + +
125G ILE 3.0 22.9 + - - -
193G LEU* 3.5 19.1 - - + +
195G MSE 4.1 9.2 - - + -
231G THR* 3.8 33.7 - - + -
235G LEU* 3.9 17.9 - - + -
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Residues in contact with ILE 99 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97G LEU* 5.2 2.2 - - + -
98G LEU* 1.3 76.9 - - - +
100G LEU* 1.3 66.3 + - - +
125G ILE* 3.4 21.1 - - + +
157G LEU* 3.7 33.0 - - + -
161G MSE 4.2 15.0 - - + -
164G LEU* 3.7 29.4 - - + -
171G ILE* 5.0 1.1 - - + -
192G ALA* 4.3 13.5 - - + -
193G LEU 2.7 16.4 + - - +
194G VAL* 3.3 30.9 - - + +
195G MSE 2.8 27.9 + - - +
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Residues in contact with LEU 100 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98G LEU* 4.0 21.1 - - + -
99G ILE* 1.3 78.4 - - - +
101G ASP* 1.3 59.4 + - - +
102G GLY 3.1 7.4 + - - -
103G VAL* 3.7 26.7 + - + +
109G LEU* 4.0 24.9 - - + -
112G CYS* 3.9 33.0 - - + -
113G LEU 5.8 0.4 - - - +
124G VAL* 4.1 18.8 - - + -
125G ILE 3.1 7.2 + - - -
126G VAL* 3.7 15.0 - - + +
127G PRO* 3.3 16.7 - - - +
195G MSE 3.6 21.8 - - + -
227G VAL* 5.6 0.4 - - + -
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Residues in contact with ASP 101 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99G ILE 3.8 1.0 + - - -
100G LEU* 1.3 67.1 - - - +
102G GLY* 1.3 61.1 + - - +
103G VAL* 3.8 0.8 - - - +
127G PRO* 4.3 9.1 - - - +
157G LEU* 3.3 14.4 - - + +
194G VAL* 4.4 4.3 - - + -
195G MSE 2.9 18.7 + - - +
196G GLY* 4.4 4.0 - - - -
197G ALA* 4.0 14.3 + - - +
201G GLY 4.2 3.1 - - - +
202G MSE 3.5 2.3 - - + -
203G ARG* 2.7 49.1 + - - +
206G THR* 3.0 34.3 + - + -
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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