Contacts of the helix formed by residues 92 - 97 (chain O) in PDB entry 2GTL
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 92 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87O ASN* 5.0 10.8 - - - -
89O CYS 3.0 12.6 + - - -
90O ARG 4.4 0.2 - - - -
91O ASN* 1.3 81.4 + - - +
93O GLU* 1.3 66.6 + - - +
94O ASP* 2.9 12.9 - - - +
95O GLU* 2.6 17.8 + - - +
96O LYS* 3.2 15.7 + - - +
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Residues in contact with GLU 93 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67O HIS* 3.3 32.3 + - - +
68O GLN 4.5 2.6 - - - +
69O CYS* 3.7 22.7 - - - +
82O VAL* 5.2 1.2 - - - +
83O CYS* 5.5 0.5 - - - -
91O ASN* 3.1 16.8 + - - +
92O GLY* 1.3 74.0 - - - +
94O ASP* 1.3 54.5 + - - +
95O GLU 2.5 14.2 + - - -
96O LYS* 3.1 28.8 + - - +
97O ASP* 3.6 28.3 + - - +
98O CYS* 5.5 0.3 - - - -
174O HIS* 5.3 7.8 + - - -
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Residues in contact with ASP 94 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67O HIS* 4.4 5.2 - - + -
69O CYS* 4.0 7.8 - - - -
77O ILE* 4.5 5.6 - - + -
82O VAL* 4.1 22.2 - - - -
83O CYS* 2.6 32.5 + - - -
87O ASN* 4.8 0.5 - - - -
88O ASP* 2.7 20.5 + - - +
89O CYS* 2.6 38.9 + - + +
92O GLY* 2.9 21.8 - - - +
93O GLU* 1.3 74.2 - - - +
95O GLU* 1.3 62.0 + - - +
250O CA 2.9 12.5 - - - -
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Residues in contact with GLU 95 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83O CYS* 3.0 4.7 + - - -
84O ASP* 2.6 38.0 + - - +
85O GLY* 3.2 20.5 + - - -
86O HIS 3.2 24.9 - - - +
87O ASN* 4.2 14.6 - - - +
92O GLY 2.6 10.5 + - - +
93O GLU 2.5 11.3 + - - -
94O ASP* 1.3 92.9 - - - +
96O LYS* 1.3 57.7 + - - -
97O ASP 3.5 2.5 - - - -
98O CYS* 3.6 17.7 - - - -
250O CA 2.8 4.9 - - - -
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Residues in contact with LYS 96 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91O ASN* 4.7 14.7 + - - +
92O GLY* 3.2 5.8 + - - +
93O GLU* 3.1 34.0 + - - +
95O GLU* 1.3 79.1 - - - +
97O ASP* 1.3 77.9 + - - +
98O CYS 3.8 2.7 + - - -
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Residues in contact with ASP 97 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83O CYS* 3.9 5.7 - - - -
93O GLU* 3.6 29.5 + - - +
95O GLU 3.5 0.2 - - - -
96O LYS* 1.3 98.0 - - - +
98O CYS* 1.3 61.8 + - - +
99O THR* 3.7 8.3 + - - +
171O PHE* 4.8 4.9 - - - +
174O HIS* 5.1 13.1 + - - +
195O TYR* 5.9 3.0 - - - -
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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