Contacts of the strand formed by residues 231 - 243 (chain A) in PDB entry 2G4C
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 ILE 231 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A GLY 4.4 1.6 - - - +
95A CYS* 3.7 12.5 - - - -
145A PHE* 3.4 36.6 - - + -
181A LEU* 5.1 2.9 - - + -
215A PHE* 4.2 25.6 - - + -
216A HIS 4.1 8.3 - - - +
217A PRO* 4.6 1.1 - - + -
229A LYS 4.9 1.8 - - - +
230A SER* 1.3 82.5 - - - +
232A GLY* 1.3 62.3 + - - +
233A GLU 4.2 0.3 + - - -
133C HIS* 2.9 52.6 - - + +
135C PRO* 4.8 9.0 - - + -
147C LEU* 4.1 15.7 - - + -
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Residues in contact with GLY 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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93A SER 3.5 17.0 - - - -
94A GLY 3.5 10.1 - - - -
95A CYS* 4.1 2.2 - - - -
214A CYS 3.5 0.3 - - - +
215A PHE* 3.2 8.3 - - - +
216A HIS* 2.7 44.0 + - - -
218A VAL* 4.4 1.2 - - - +
230A SER 4.3 0.2 + - - -
231A ILE* 1.3 75.1 - - - +
233A GLU* 1.3 63.4 + - - -
234A LYS* 5.4 1.8 - - - -
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Residues in contact with GLU 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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94A GLY* 3.0 23.4 + - - +
96A HIS* 4.6 7.3 + - - +
213A VAL* 3.9 6.2 - - + +
214A CYS 3.5 2.9 - - - -
215A PHE* 3.5 29.4 - - + -
232A GLY* 1.3 73.3 - - - -
234A LYS* 1.3 67.6 + - - +
343A ASP* 4.4 4.2 - - - +
131C LEU* 3.7 24.5 - - + +
132C HIS* 2.8 47.3 + - - +
133C HIS* 3.0 31.8 + - + +
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Residues in contact with LYS 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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91A LEU 5.5 0.6 + - - -
92A LEU 3.0 28.2 + - - -
93A SER* 4.3 12.1 - - - +
94A GLY* 4.5 5.0 - - - +
212A GLY 3.5 0.3 - - - +
213A VAL* 3.0 5.8 - - - +
214A CYS* 2.6 42.0 + - - +
216A HIS* 3.6 30.5 - - + +
232A GLY 5.4 1.3 - - - -
233A GLU* 1.3 80.1 - - - +
235A THR* 1.3 61.7 + - - +
236A GLU* 3.5 7.1 + - + -
341A ASP* 3.1 38.5 + - - +
343A ASP* 3.6 8.7 - - + +
344A ARG* 3.1 16.8 - - - +
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Residues in contact with THR 235 (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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107A ARG* 3.0 29.1 + - - -
211A ILE* 4.1 16.2 - - + -
212A GLY* 3.3 8.5 - - - +
213A VAL* 3.7 17.3 - - - +
234A LYS* 1.3 69.8 - - - +
236A GLU* 1.3 59.4 + - - +
341A ASP* 4.0 1.0 - - - +
342A LEU* 2.9 52.0 + - + +
343A ASP* 2.7 20.4 + - - +
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Residues in contact with GLU 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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183A GLU 3.6 5.0 - - - +
184A ASN* 4.2 5.5 - - - +
185A LEU* 3.6 8.3 + - + +
211A ILE* 3.2 3.0 - - - +
212A GLY 2.6 43.0 + - - +
214A CYS* 3.3 32.2 - - + +
216A HIS* 3.3 25.8 + - - -
234A LYS* 4.0 12.1 - - + +
235A THR* 1.3 79.5 - - - +
237A ALA* 1.3 60.4 + - - +
238A SER 4.0 0.4 - - - -
339A ASN* 3.2 26.4 - - - +
340A GLY 3.3 9.3 - - - +
341A ASP* 4.2 13.7 - - - +
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Residues in contact with ALA 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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114A TRP* 3.5 40.3 + - + +
210A GLN 3.5 4.5 - - - -
211A ILE* 3.6 16.8 - - + -
235A THR 4.2 0.2 + - - -
236A GLU* 1.3 72.1 - - - +
238A SER* 1.3 58.9 + - - +
301A GLU* 5.0 0.3 - - - +
338A VAL 3.8 0.9 - - - +
339A ASN* 3.5 5.2 - - - +
340A GLY* 3.0 34.2 + - - +
342A LEU* 4.3 12.3 - - + -
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Residues in contact with SER 238 (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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114A TRP* 4.1 4.8 - - - -
185A LEU* 3.5 35.9 + - - +
186A LEU* 4.5 0.7 + - - -
189A ALA* 5.6 0.2 - - - +
208A LEU 3.6 2.1 - - - +
209A ALA* 3.2 3.1 - - - -
210A GLN* 2.6 41.2 + - - +
236A GLU 4.0 0.4 - - - -
237A ALA* 1.3 73.9 - - - +
239A LEU* 1.3 60.8 + - - +
240A VAL* 3.9 17.2 - - - +
337A SER* 5.0 1.4 + - - -
338A VAL 3.4 8.2 + - - -
339A ASN* 3.8 17.2 + - - -
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Residues in contact with LEU 239 (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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114A TRP* 4.2 16.8 - - + -
118A VAL* 3.5 30.7 - - + -
125A VAL* 4.1 11.2 - - + -
207A GLY* 4.0 23.6 - - - -
208A LEU 3.8 4.5 - - - +
209A ALA* 4.3 0.9 - - + +
238A SER* 1.3 72.4 - - - +
240A VAL* 1.3 68.3 + - - +
241A TRP* 3.9 10.3 + - + +
255A TRP* 3.6 39.3 - - + -
259A ARG* 6.3 0.4 - - - -
337A SER* 3.8 0.7 - - - -
338A VAL* 2.9 47.7 + - + +
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Residues in contact with VAL 240 (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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186A LEU* 4.5 14.8 - - + -
189A ALA* 3.5 28.7 - - + -
190A LEU* 4.2 6.7 - - + -
207A GLY* 3.1 6.2 - - - -
208A LEU* 3.1 31.8 + - + +
238A SER* 3.9 13.7 - - - +
239A LEU* 1.3 78.3 - - - +
241A TRP* 1.3 61.1 + - - +
242A PHE* 3.8 24.7 + - + -
335A VAL* 3.6 22.4 - - + -
336A LEU 3.6 11.4 - - - +
337A SER* 4.6 5.6 - - - +
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Residues in contact with TRP 241 (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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122A ARG* 5.2 0.9 - - - -
124A GLN* 3.5 32.3 - - + -
125A VAL* 3.6 19.1 - - + -
205A PRO* 3.8 24.2 - - + +
206A TYR* 4.2 5.2 - - - -
207A GLY* 3.2 34.8 - - - -
239A LEU* 3.9 13.9 + - + +
240A VAL* 1.3 71.2 - - - +
242A PHE* 1.3 61.1 + - - +
243A THR* 3.4 29.6 + - + -
251A TRP* 3.2 42.2 - + + -
255A TRP* 3.7 34.8 - + + +
334A CYS 3.4 0.9 - - - +
335A VAL* 3.8 1.9 - - - -
336A LEU* 3.0 47.0 + - + +
338A VAL* 6.1 0.7 - - + -
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Residues in contact with PHE 242 (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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189A ALA 4.6 5.4 - - - -
190A LEU* 4.2 13.0 - - + -
193A TYR* 3.4 44.4 - + + -
204A LEU* 3.7 9.8 - - + +
205A PRO* 3.1 22.6 - - - +
206A TYR* 3.0 61.9 + + + +
208A LEU* 3.6 27.1 - - + -
240A VAL* 3.9 25.8 - - + -
241A TRP* 1.3 72.4 - - - +
243A THR* 1.3 57.8 + - - +
311A LEU* 4.5 4.3 - - + -
333A PRO* 4.1 8.7 - - + -
334A CYS 3.8 4.0 - - - -
335A VAL* 4.3 15.9 - - + -
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Residues in contact with THR 243 (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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205A PRO* 3.7 3.6 - - - -
241A TRP* 3.7 24.0 - - + +
242A PHE* 1.3 74.6 - - - +
244A PRO* 1.3 78.1 + - - +
247A THR* 3.7 0.5 - - - -
248A SER* 3.6 19.6 + - - +
251A TRP* 3.0 29.8 - - + -
333A PRO* 4.2 1.8 - - - -
334A CYS* 2.5 43.0 + - - +
336A LEU* 4.2 13.2 - - + -
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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