Contacts of the strand formed by residues 232 - 240 (chain A) in PDB entry 4FYT
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 GLU 232 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83A ASP 3.2 19.1 + - - +
84A SER* 3.2 14.6 - - - -
85A TYR 2.9 26.4 + - - -
231A ALA* 1.3 76.4 - - - +
233A PHE* 1.3 63.2 + - - +
234A ASN* 4.8 0.4 - - - +
271A THR* 3.6 20.6 - - + -
272A THR* 3.4 20.0 - - - +
273A PRO* 4.0 0.4 - - + -
274A LYS* 3.5 36.6 + - - +
1C NAG 5.7 0.4 - - - -
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Residues in contact with PHE 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A TYR* 3.1 47.6 - + + -
87A VAL* 5.1 0.4 - - + -
221A PHE* 3.9 12.3 - + - -
229A MET 5.4 0.4 - - - -
231A ALA* 3.3 24.7 - - + -
232A GLU* 1.3 73.1 - - - +
234A ASN* 1.3 65.0 + - - +
235A ILE* 3.9 12.6 + - + +
270A HIS 4.1 1.2 - - - +
271A THR* 3.5 1.4 - - - -
272A THR* 2.9 45.8 + - + +
275A MET* 3.6 21.3 - - + -
276A SER 4.6 0.2 - - - -
277A THR* 3.6 26.2 - - + -
280A LEU* 3.7 44.9 - - + -
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Residues in contact with ASN 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A TYR 2.8 13.3 + - - +
86A ARG* 3.2 10.5 - - + +
87A VAL 3.0 25.3 + - - +
232A GLU 4.8 0.2 - - - -
233A PHE* 1.3 70.6 - - - +
235A ILE* 1.3 63.1 + - - +
236A THR* 3.9 1.3 + - - -
268A GLU* 5.3 10.3 - - - +
269A PHE 4.7 4.7 - - - +
271A THR* 2.8 30.9 + - - +
1C NAG 1.4 66.3 + - - +
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Residues in contact with ILE 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A VAL* 3.5 23.1 - - + +
89A LEU* 6.3 0.7 - - + -
233A PHE* 3.9 26.5 + - + +
234A ASN* 1.3 77.0 - - - +
236A THR* 1.3 63.1 + - - +
237A LEU* 4.1 16.4 - - + -
247A SER* 3.9 16.6 - - - +
268A GLU* 3.9 0.7 - - - +
269A PHE* 2.8 51.7 + - + +
270A HIS 5.1 0.2 + - - -
272A THR* 5.2 4.3 - - + -
280A LEU* 4.5 7.0 - - + -
282A PHE* 3.5 47.3 - - + -
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Residues in contact with THR 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A VAL 2.9 7.9 + - - +
88A THR* 3.3 30.0 + - + +
89A LEU 3.0 24.6 + - - +
234A ASN 5.0 1.6 + - - -
235A ILE* 1.3 74.2 - - - +
237A LEU* 1.3 71.2 + - - +
238A ILE* 4.5 0.9 - - + -
266A VAL* 3.6 31.4 - - + -
267A THR 3.3 9.4 - - - +
268A GLU* 3.6 20.8 - - + +
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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
----------------------------------------------------------
89A LEU* 3.4 23.8 - - + +
91A PRO* 5.7 0.9 - - + -
193A PHE* 5.0 5.4 - - + -
235A ILE* 4.1 11.0 - - + -
236A THR* 1.3 82.0 - - - +
238A ILE* 1.3 63.0 + - - +
239A HIS* 3.3 7.6 - - + -
245A ALA* 3.9 23.1 - - + -
246A LEU 3.6 24.2 - - - +
247A SER* 4.9 0.4 - - - -
266A VAL* 3.7 0.3 - - - -
267A THR 2.8 33.3 + - - +
269A PHE* 3.9 15.5 - - + -
282A PHE* 3.9 27.1 - - + -
283A ILE 4.1 7.0 - - - +
284A VAL* 4.4 11.0 - - + -
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Residues in contact with ILE 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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88A THR* 3.6 30.5 - - + -
89A LEU 3.0 4.9 + - - -
90A ARG* 3.5 42.3 - - + +
91A PRO* 3.4 23.1 - - - +
236A THR* 4.5 0.2 - - + -
237A LEU* 1.3 74.6 - - - +
239A HIS* 1.3 63.2 + - - +
258A LEU* 4.2 30.7 - - + -
260A GLU* 5.9 0.4 - - - +
264A TRP* 3.8 11.1 - - + -
265A ASN 3.3 10.1 - - - +
266A VAL* 4.2 17.9 - - + -
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Residues in contact with HIS 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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91A PRO* 5.1 0.9 - - + -
237A LEU 3.3 20.0 - - - -
238A ILE* 1.3 76.4 - - - +
240A PRO* 1.3 82.9 + - + +
243A LEU 2.9 29.3 + - - -
245A ALA* 3.7 20.7 + - + +
264A TRP* 3.2 8.1 - - - -
265A ASN* 2.7 59.7 + - + +
267A THR* 2.7 27.7 + - - -
284A VAL* 3.8 23.6 - - + -
1004A NAG 3.7 10.8 - - - -
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Residues in contact with PRO 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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91A PRO* 4.8 3.4 - - + +
93A LEU* 4.4 17.5 - - + +
239A HIS* 1.3 97.3 + - + +
241A LYS* 1.3 60.8 + - - +
242A ASP* 3.1 15.7 - - - +
243A LEU* 2.9 46.2 + - + -
263A ASN 3.6 8.5 - - - +
264A TRP* 3.6 24.7 - - + -
284A VAL* 4.6 0.7 - - + -
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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