Contacts of the strand formed by residues 234 - 244 (chain B) in PDB entry 3GGS
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 234 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109B ASP* 2.8 33.2 + - - +
110B THR* 3.3 27.4 + - + +
111B LEU* 2.6 33.6 + - - +
167B ASP* 3.6 41.2 + - + +
169B THR* 6.1 1.0 - - - -
170B MET* 3.9 17.0 - - + -
229B ARG* 4.5 3.8 - - - +
232B GLY 3.7 1.6 + - - -
233B LEU* 1.3 72.9 - - - +
235B VAL* 1.3 56.4 + - - +
282B ILE* 4.4 0.4 - - - +
283B PRO* 3.7 46.4 + - - +
284B LEU 4.8 2.6 + - - -
291B SO4 5.1 4.7 - - - +
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Residues in contact with VAL 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B LEU* 3.2 14.1 - - + +
113B VAL* 4.5 4.7 - - + -
165B ALA 3.5 13.3 + - - +
166B TYR* 3.7 11.8 - - + -
167B ASP* 3.0 30.0 + - - +
225B VAL* 4.0 29.4 - - + +
228B ALA* 3.7 30.3 - - + -
229B ARG* 3.8 13.0 - - + +
233B LEU 3.5 9.1 + - - +
234B ARG* 1.3 80.7 - - - +
236B PHE* 1.3 73.4 + - - +
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Residues in contact with PHE 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B THR* 3.9 26.0 - - + -
111B LEU 3.1 6.4 + - - +
112B VAL* 3.0 33.3 - - + +
113B VAL* 3.0 24.2 + - - +
131B LEU* 5.2 7.4 - - + -
132B ILE 5.7 0.2 - - - -
166B TYR* 4.6 6.5 - - - +
167B ASP* 5.2 2.9 - - + +
170B MET* 3.7 56.8 - - + -
171B ARG* 5.4 2.9 - - + -
174B ALA* 5.8 0.4 - - + -
234B ARG* 5.3 0.2 - - - -
235B VAL* 1.3 81.4 - - - +
237B GLY* 1.3 62.4 + - - +
238B PHE* 4.1 26.5 - + - -
275B VAL* 6.1 1.6 - - + -
278B LEU* 4.3 15.5 - - + -
279B MET* 4.7 6.7 - - + -
282B ILE* 4.1 12.6 - - + -
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Residues in contact with GLY 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B VAL* 5.1 0.9 - - - -
113B VAL* 2.9 21.3 - - - +
131B LEU* 3.5 6.3 - - - +
132B ILE* 3.1 28.7 + - - -
166B TYR* 4.8 4.8 - - - -
236B PHE* 1.3 80.9 - - - +
238B PHE* 1.3 77.4 + - - -
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Residues in contact with PHE 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B VAL* 5.4 2.5 - - + -
113B VAL 2.9 7.8 + - - +
114B THR* 3.4 7.6 - - + -
115B ASN* 3.0 27.7 + - - +
129B ILE* 3.6 27.8 - - + -
130B MET 3.2 6.3 - - - +
131B LEU* 3.9 34.3 - - + -
132B ILE* 3.9 4.8 - - - +
174B ALA* 4.3 3.1 - - + -
187B LEU* 4.7 1.8 - - + -
236B PHE* 4.1 17.9 - + - -
237B GLY* 1.3 83.0 - - - -
239B SER* 1.3 61.3 + - - +
271B LEU* 4.2 26.2 - - + +
274B PHE* 3.6 19.5 - + - -
275B VAL* 4.5 14.1 - - + -
278B LEU* 3.5 31.9 - - + -
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Residues in contact with SER 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B ASN* 2.5 29.0 + - - -
117B ALA* 3.8 15.7 - - - -
129B ILE* 3.5 3.3 - - - -
130B MET* 2.8 52.9 + - - +
132B ILE* 3.9 6.0 - - - +
192B TYR* 3.5 17.0 - - - -
238B PHE* 1.3 73.6 - - - +
240B LEU* 1.3 60.9 + - - +
241B ILE* 3.7 4.8 + - - +
271B LEU* 5.1 0.4 - - - -
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Residues in contact with LEU 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B LEU* 4.2 8.5 - - + -
115B ASN 2.8 15.3 + - - +
116B ALA* 3.4 6.0 - - + -
117B ALA 2.9 21.8 + - - -
127B GLY* 3.8 14.1 - - - +
128B ASP 3.6 14.6 - - - +
129B ILE* 4.1 11.0 - - + +
238B PHE 4.2 0.4 - - - -
239B SER* 1.3 70.4 - - - +
241B ILE* 1.3 63.5 + - - +
242B THR* 3.1 7.7 + - + +
263B ALA* 3.3 34.8 - - + -
267B ALA* 3.7 23.8 - - + +
268B ALA* 3.7 23.8 - - + +
271B LEU* 4.1 14.7 - - + +
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Residues in contact with ILE 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B ALA* 3.4 12.3 - - + +
118B GLY 4.6 1.3 - - - +
119B GLY* 3.8 13.0 - - - +
124B PHE* 3.9 33.0 - - + -
125B GLU 4.0 20.9 - - - +
126B VAL* 3.5 0.6 - - - -
127B GLY* 2.8 30.5 + - - -
128B ASP* 2.8 30.2 + - + +
130B MET* 4.5 4.7 - - + -
216B ALA* 4.2 20.0 - - + -
239B SER* 4.2 10.3 - - - +
240B LEU* 1.3 71.7 - - - +
242B THR* 1.3 58.5 + - - +
243B ASP 3.5 23.8 - - - +
244B LYS* 5.3 1.3 - - + -
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Residues in contact with THR 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B ALA* 3.6 24.9 - - + -
117B ALA 2.9 15.8 + - - -
126B VAL* 3.2 22.2 - - - +
240B LEU* 3.8 7.0 - - + +
241B ILE* 1.3 73.0 - - - +
243B ASP* 1.3 62.8 + - - +
261B LEU* 4.0 18.9 + - - +
262B ALA* 4.2 4.7 - - - +
263B ALA* 3.6 34.5 - - + +
300B 2FD 3.5 21.1 - - - -
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Residues in contact with ASP 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B ALA 4.1 0.2 + - - -
118B GLY* 3.6 1.4 - - - -
119B GLY 2.8 23.0 + - - -
126B VAL* 4.9 5.6 - - - -
241B ILE* 3.5 8.3 - - - +
242B THR* 1.3 75.9 + - - +
244B LYS* 1.3 79.7 + - - +
245B VAL* 4.1 5.0 + - - +
259B GLU 5.5 1.3 - - - +
260B VAL* 3.2 39.1 - - + +
261B LEU 5.4 0.4 - - - +
300B 2FD 2.7 35.0 + - - -
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Residues in contact with LYS 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B GLY* 3.8 9.2 - - - +
121B ASN 5.3 2.7 - - - +
122B PRO* 3.7 21.6 + - - +
124B PHE* 3.0 25.3 + - + +
125B GLU* 4.2 19.1 + - + +
126B VAL* 4.5 13.9 - - + +
241B ILE* 5.3 2.0 - - + -
243B ASP* 1.3 86.1 - - - +
245B VAL* 1.3 66.0 + - - +
246B ILE* 3.7 10.5 + - + +
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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