Contacts of the strand formed by residues 198 - 203 (chain G) in PDB entry 1GHB
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 PRO 198 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29F TRP* 4.2 12.1 - - + +
30F GLN* 3.4 25.1 - - - +
44F GLY 3.9 6.7 - - - +
45F SER* 3.2 28.9 - - - +
137F VAL 3.7 0.7 - - - +
138F THR* 3.3 26.4 + - - -
139F THR* 3.6 13.0 + - - +
197G GLY* 1.3 85.8 - - - +
199G LEU* 1.3 60.4 + - - +
200G VAL* 3.9 12.5 - - + +
209G LEU* 4.0 14.4 - - + -
211G GLY 3.7 4.0 - - - +
213G VAL* 4.8 0.7 - - - -
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Residues in contact with LEU 199 (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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136F CYS* 4.0 15.9 - - + -
137F VAL 3.4 11.7 - - - +
138F THR* 4.3 4.7 - - - -
160G LEU* 3.8 26.5 - - + -
162G LEU* 3.8 24.0 - - + -
181G ILE* 4.8 4.7 - - + -
183G ALA* 4.5 4.0 - - + -
198G PRO* 1.3 71.2 - - - +
200G VAL* 1.3 59.8 + - - +
209G LEU* 3.8 3.1 - - - +
210G VAL* 2.9 32.4 + - + -
211G GLY* 2.9 30.5 + - - +
228G TYR* 3.9 36.6 - - + -
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Residues in contact with VAL 200 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27F TRP* 4.2 12.8 - - + -
29F TRP* 4.1 13.7 - - + +
121F VAL* 3.6 30.5 - - + -
136F CYS* 2.9 2.9 - - - +
137F VAL* 2.7 54.2 + - + +
139F THR* 6.4 0.2 - - + -
198G PRO* 4.4 12.1 - - + +
199G LEU* 1.3 78.5 - - - +
201G CYS* 1.3 62.6 + - - +
207G TRP* 3.4 31.1 - - + -
208G THR 3.6 8.7 - - - +
209G LEU* 4.5 2.0 - - - +
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Residues in contact with CYS 201 (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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130F PHE* 3.6 24.9 - - + -
134F THR* 5.2 3.8 - - + -
135F THR 5.1 2.0 - - - +
136F CYS* 2.0 48.7 - - - +
162G LEU* 4.4 2.7 - - - -
199G LEU* 5.0 0.7 - - - -
200G VAL* 1.3 72.6 - - - +
202G LYS* 1.3 62.2 + - - +
207G TRP* 3.8 6.5 - - - -
208G THR* 2.9 31.6 + - - +
210G VAL* 3.2 30.7 - - + -
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Residues in contact with LYS 202 (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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130F PHE* 4.9 0.2 - - - -
134F THR* 6.1 0.7 - - - +
135F THR 5.5 1.2 + - - -
201G CYS* 1.3 76.2 - - - +
203G LYS* 1.3 65.1 + - - +
204G ASN 4.2 0.2 - - - -
205G GLY* 4.1 23.6 - - - -
206G ALA 3.4 12.8 - - - +
207G TRP* 3.5 53.4 - - + +
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Residues in contact with LYS 203 (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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128F ASP* 3.7 19.5 + - - +
129F ASP* 3.1 40.9 + - - +
130F PHE* 3.6 21.7 - - + -
201G CYS 3.8 0.4 + - - -
202G LYS* 1.3 76.1 - - - +
204G ASN* 1.3 87.2 + - - +
206G ALA* 3.0 21.5 + - - +
208G THR* 3.5 20.6 - - + +
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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