Contacts of the strand formed by residues 229 - 237 (chain A) in PDB entry 3GBN
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 ARG 229 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A TYR* 3.8 3.1 - - - -
99A PRO* 3.4 24.0 - - - +
100A GLY* 4.3 9.7 - - - +
183A HIS* 3.4 4.3 - - - -
184A HIS* 2.8 43.1 + - + +
220A ARG* 3.7 19.8 - - + +
221A PRO* 3.1 45.9 + - - +
223A VAL* 3.4 20.1 - - - +
228A GLY* 1.3 81.7 + - - -
230A MET* 1.3 62.0 + - - +
231A ASN* 4.4 3.8 - - - +
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Residues in contact with MET 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A TYR* 3.4 50.0 - - + -
99A PRO 2.6 9.2 + - - +
100A GLY* 3.1 13.2 - - - -
147A PHE* 4.2 12.6 - - + -
153A TRP* 3.8 21.5 - - + -
182A VAL 3.7 11.9 - - - +
183A HIS* 4.0 13.7 - - + -
229A ARG* 1.3 73.1 - - - +
231A ASN* 1.3 65.0 + - - +
232A TYR* 3.1 44.3 - - + +
252A ILE* 3.6 28.5 - - + -
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Residues in contact with ASN 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A GLY* 4.0 2.3 - - - -
101A ASP* 3.1 40.1 + - - +
103A ILE* 4.8 5.3 - - + +
181A GLY* 3.1 4.5 - - - -
182A VAL 2.8 36.7 + - - +
184A HIS* 3.5 27.3 + - - +
229A ARG* 5.2 2.3 - - - +
230A MET* 1.3 74.9 + - - +
232A TYR* 1.3 61.0 + - - +
233A TYR* 3.4 31.7 + - + +
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Residues in contact with TYR 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A LEU* 3.8 22.4 - - + -
96A THR* 3.2 26.9 - - + -
98A TYR* 2.4 33.3 + - - +
100A GLY 4.4 2.5 - - - -
101A ASP 3.0 14.6 + - - -
102A PHE* 4.0 25.7 - - + -
103A ILE* 3.0 27.6 + - - +
148A TYR* 2.6 37.9 + + - -
151A LEU* 4.3 13.0 - - + -
180A TRP 3.6 4.3 - - - +
181A GLY* 4.6 2.0 - - - -
230A MET* 3.1 36.4 - - + +
231A ASN* 1.3 75.4 - - - +
233A TYR* 1.3 66.2 + - - +
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Residues in contact with TYR 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A LEU* 5.9 0.3 - - - +
102A PHE* 4.9 1.6 - - - -
103A ILE* 3.4 37.8 - - + +
179A LEU* 3.3 7.8 - - - +
180A TRP* 2.9 68.0 + + + +
182A VAL* 4.3 10.8 - - + -
184A HIS* 5.1 2.1 + - - -
209A TYR* 4.1 7.9 - - - +
211A ARG* 4.1 13.1 + - - -
213A PHE* 3.4 40.0 - + - -
231A ASN* 3.4 45.0 + - + +
232A TYR* 1.3 77.4 - - - +
234A TRP* 1.3 66.2 + - - +
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Residues in contact with TRP 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A PHE* 3.8 15.5 - + - -
103A ILE 3.2 17.8 + - - -
104A ASP* 3.1 36.2 + - + +
107A GLU* 4.0 10.5 - - + -
108A LEU* 3.7 26.1 - - + +
111A GLN* 4.1 22.7 - - + -
177A LEU* 3.9 18.4 - - + -
178A VAL 3.1 9.6 - - - +
179A LEU* 3.7 20.2 - - + -
180A TRP* 4.0 8.5 - - - -
209A TYR* 4.5 7.4 + - - -
233A TYR* 1.3 74.4 - - - +
235A THR* 1.3 73.6 + - - +
236A LEU* 4.0 25.6 - - + -
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Residues in contact with THR 235 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176A VAL 3.6 1.0 - - - +
177A LEU* 3.6 3.3 - - - +
178A VAL* 2.9 36.3 + - + +
180A TRP* 4.0 11.7 - - + -
206A SER* 5.4 3.0 + - - +
208A LYS* 4.4 8.0 - - - +
209A TYR* 3.9 34.0 - - + +
234A TRP* 1.3 88.8 - - - +
236A LEU* 1.3 66.3 + - - +
237A LEU* 4.6 8.3 - - + +
243A ILE* 3.8 28.9 - - + -
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Residues in contact with LEU 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A LEU* 5.9 0.7 - - + -
111A GLN* 3.5 40.4 - - + +
175A GLU* 3.9 21.1 - - + +
176A VAL 3.4 3.8 - - - +
177A LEU* 3.9 21.3 - - + -
208A LYS* 3.2 33.3 - - + +
234A TRP* 4.0 16.2 - - + -
235A THR* 1.3 76.2 + - - +
237A LEU* 1.3 63.8 + - - +
238A GLU* 4.6 0.5 - - - +
260A LEU* 3.4 32.8 - - + -
262A ARG* 3.6 11.2 - - - +
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Residues in contact with LEU 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A TYR* 3.8 19.1 - - + +
170A ASN* 3.0 29.8 + - + -
175A GLU* 3.5 3.3 - - - -
176A VAL* 2.7 32.0 + - + +
178A VAL* 4.7 8.5 - - + -
206A SER* 4.5 7.2 - - - +
208A LYS* 6.4 0.7 - - - -
235A THR* 3.8 7.3 + - + +
236A LEU* 1.3 70.5 - - - +
238A GLU* 1.3 69.0 + - - +
241A ASP* 3.6 44.6 - - + +
242A THR 3.9 8.7 - - - +
243A ILE* 3.8 30.7 - - + +
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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