Contacts of the strand formed by residues 202 - 210 (chain A) in PDB entry 4KXA
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 GLY 202 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201A VAL* 1.3 76.4 - - - +
203A PHE* 1.3 59.5 + - - -
204A TYR* 3.9 1.9 - - - -
219A ALA 3.7 0.9 - - - +
220A THR* 3.0 4.5 - - - -
221A ASP 2.9 37.6 + - - -
226A ASP* 3.9 14.5 - - - +
229A LYS* 4.2 6.7 - - - -
230A SER* 3.1 22.9 - - - -
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Residues in contact with PHE 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A VAL* 4.5 10.3 - - + -
108A PRO* 4.2 19.3 - - + -
115A TYR* 3.6 52.3 + + + -
195A TRP 3.3 21.3 - - - +
196A LEU* 3.5 14.4 - - + +
201A VAL 4.5 1.6 - - - +
202A GLY* 1.3 70.7 - - - -
204A TYR* 1.3 63.0 + - - +
218A ALA* 3.8 29.6 - - + -
219A ALA* 3.3 17.7 - - - -
220A THR* 3.6 9.6 - - + -
229A LYS* 4.7 3.5 + - - +
230A SER* 3.1 11.2 + - - +
289A PHE* 3.6 37.9 - + + -
290A ALA* 5.4 1.1 - - - -
291A VAL* 5.1 5.4 - - + -
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Residues in contact with TYR 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A LEU* 3.4 22.0 - - - +
199A SER* 3.4 23.1 - - - +
200A LEU* 3.4 39.4 + - + -
201A VAL 4.2 4.3 - - - +
202A GLY 3.9 9.9 - - - -
203A PHE* 1.3 75.3 - - - +
205A ARG* 1.3 69.3 + - - +
206A THR* 4.4 7.4 - - + -
217A ILE 4.1 0.2 - - - +
218A ALA* 3.1 3.3 - - - +
219A ALA* 2.9 52.0 + - + +
220A THR 4.6 0.7 - - - -
221A ASP* 4.5 8.7 - - + -
229A LYS* 5.6 0.7 - - - +
351A ILE* 3.4 22.2 - - + +
353A ASP 2.9 28.6 + - - -
354A PHE* 3.6 17.7 - + - -
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Residues in contact with ARG 205 (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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110A LEU* 3.1 41.1 + - + +
111A GLU* 4.2 18.2 + - - -
113A ASP* 2.7 43.9 + - - +
196A LEU* 2.9 24.5 + - + +
197A ASN* 5.4 1.2 - - - -
199A SER 5.4 0.3 - - - +
204A TYR* 1.3 79.6 - - - +
206A THR* 1.3 70.5 + - - +
207A THR* 3.6 21.0 - - - +
214A VAL* 5.9 0.4 - - - +
216A SER* 2.7 36.5 + - - +
217A ILE 3.4 11.7 - - - +
218A ALA* 4.2 2.9 - - + +
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Residues in contact with THR 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A LEU* 5.8 1.6 - - - -
204A TYR* 4.4 6.5 - - + -
205A ARG* 1.3 76.9 - - - +
207A THR* 1.3 73.8 + - - +
216A SER* 3.5 3.6 - - - -
217A ILE* 2.9 50.7 + - + +
351A ILE* 3.8 22.7 - - + -
352A PRO* 4.0 4.0 - - + -
353A ASP* 3.4 37.7 + - + +
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Residues in contact with THR 207 (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 ARG* 3.6 28.5 - - - +
206A THR* 1.3 84.3 + - - +
208A TYR* 1.3 68.2 + - - +
214A VAL* 3.9 22.1 - - + +
215A LYS 3.1 15.9 - - - +
216A SER* 4.1 0.4 - - - +
352A PRO* 3.9 12.5 - - - +
846A LYS* 5.2 6.1 + - - -
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Residues in contact with TYR 208 (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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207A THR* 1.3 79.6 - - - +
209A THR* 1.3 68.4 + - - +
210A GLU* 4.1 19.9 + - + -
214A VAL* 3.6 4.1 - - - +
215A LYS* 2.7 63.7 + - + +
216A SER 4.2 7.6 + - - -
217A ILE* 4.2 11.4 - - + -
293A GLN* 4.0 14.7 + - - +
294A PHE* 3.4 34.9 - + - -
312A GLN* 3.4 38.6 - - + +
313A PRO* 5.5 0.3 - - - +
352A PRO* 3.9 19.1 - - + -
846A LYS* 5.9 1.8 - - - +
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Residues in contact with THR 209 (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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208A TYR* 1.3 81.7 - - - +
210A GLU* 1.3 66.0 + - - +
212A GLY* 3.8 27.1 - - - +
213A ARG 3.3 10.7 + - - +
214A VAL* 4.8 9.4 - - + +
312A GLN* 4.5 3.8 - - - +
314A GLU* 4.2 14.7 - - - +
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Residues in contact with GLU 210 (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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208A TYR* 4.1 20.8 + - + -
209A THR* 1.3 76.2 - - - +
211A ASN* 1.3 83.9 + - + +
212A GLY 3.1 0.7 - - - -
213A ARG* 2.8 28.3 + - - +
215A LYS* 3.4 34.8 + - + +
293A GLN 5.0 2.1 - - - +
312A GLN* 5.2 1.1 - - - +
313A PRO* 3.4 36.2 - - + +
314A GLU* 4.6 14.4 + - + +
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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