Contacts of the strand formed by residues 98 - 103 (chain G) in PDB entry 2R92
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 GLY 98 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94G CYS* 3.5 0.4 - - - -
95G SER* 2.7 36.9 + - - -
97G HIS* 1.3 82.7 - - - +
99G PHE* 1.3 57.2 + - - -
109G PHE* 3.5 8.0 - - - -
110G VAL 3.3 11.7 - - - -
112G LYS* 4.0 4.3 - - - -
115G MET* 4.5 1.8 - - - -
130G TYR* 2.9 20.9 + - - -
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Residues in contact with PHE 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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91G VAL* 3.7 13.0 - - + -
93G SER 3.5 11.7 - - - +
94G CYS* 3.7 14.1 - - + +
98G GLY* 1.3 75.0 - - - -
100G GLU* 1.3 61.5 + - - +
101G VAL* 3.7 16.6 - - + -
109G PHE* 2.8 17.3 - - - -
110G VAL* 3.0 34.4 + - + -
115G MET* 3.1 28.5 - - + -
119G LEU* 5.5 0.2 - - + -
130G TYR* 5.0 7.9 - + - -
137G ILE* 4.2 21.1 - - + -
143G ILE* 3.3 32.8 - - + -
145G VAL* 4.8 0.2 - - + -
163G ILE* 3.4 28.5 - - + -
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Residues in contact with GLU 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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91G VAL* 4.1 1.6 - - - -
92G VAL* 2.9 27.8 + - + +
93G SER* 2.8 34.8 + - - +
99G PHE* 1.3 74.4 - - - +
101G VAL* 1.3 65.5 + - - +
107G LYS* 3.9 36.9 + - + +
108G VAL 3.5 15.9 - - - +
109G PHE* 3.7 22.6 - - + +
158G HIS* 4.4 8.8 + - - -
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Residues in contact with VAL 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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89G GLY* 3.5 38.8 - - - +
90G THR 3.4 5.4 - - - +
91G VAL* 3.9 4.7 - - + +
92G VAL* 4.7 0.2 - - - -
99G PHE* 3.7 28.9 - - + -
100G GLU* 1.3 74.8 - - - +
102G GLN* 1.3 63.7 + - - +
103G VAL* 4.0 10.1 - - + -
107G LYS* 3.5 3.5 - - - -
108G VAL* 2.7 40.0 + - + +
110G VAL* 4.9 0.7 - - + -
143G ILE* 4.0 14.6 - - + -
145G VAL* 3.9 23.8 - - + -
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Residues in contact with GLN 102 (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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139D LYS* 5.7 3.4 + - - +
143D ASN* 3.5 30.1 + - - +
147D TYR* 3.9 5.4 - - - +
89G GLY* 3.6 1.9 - - - -
90G THR* 2.6 30.0 + - - +
92G VAL* 3.5 23.3 - - + +
101G VAL* 1.3 74.2 - - - +
103G VAL* 1.3 61.6 + - - +
104G GLY 3.4 19.0 + - - +
105G PRO* 5.4 1.1 - - - +
106G MET 3.0 17.9 - - - +
107G LYS* 3.1 32.6 - - + +
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Residues in contact with VAL 103 (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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147D TYR* 3.2 27.1 - - + +
2G PHE* 6.1 1.3 - - + -
79G PHE* 3.7 9.2 - - + -
87G VAL* 3.6 37.0 - - + +
88G ASP 3.7 3.6 - - - -
89G GLY* 3.5 28.0 - - - +
101G VAL* 4.0 10.0 + - + -
102G GLN* 1.3 71.3 - - - +
104G GLY* 1.3 64.3 + - - +
106G MET* 3.0 38.7 + - + +
107G LYS* 4.8 0.4 - - - +
108G VAL* 4.7 9.1 - - + +
145G VAL* 6.1 1.1 - - + -
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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