Contacts of the strand formed by residues 243 - 251 (chain P) in PDB entry 2D2I
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 SER 243 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208O ILE* 5.1 0.9 - - - -
181P THR 3.6 11.2 - - - -
182P HIS* 3.2 12.9 - - - -
183P SER 3.2 20.3 + - - -
242P VAL* 1.3 72.2 - - - +
244P VAL* 1.3 63.3 + - - +
315P TRP* 3.3 11.5 - - - -
316P TYR* 2.8 58.2 + - - -
318P ASN* 3.0 15.8 + - - -
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Residues in contact with VAL 244 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208O ILE* 4.7 3.1 - - + -
235O LEU* 4.1 17.0 - - + -
179P THR 3.8 0.7 - - - +
180P THR* 3.5 1.3 - - - -
181P THR* 3.0 46.7 + - + +
243P SER* 1.3 79.5 - - - +
245P VAL* 1.3 64.0 + - - +
246P ASP* 5.4 0.8 - - + +
313P ILE* 3.4 32.5 - - + -
314P ALA 3.5 16.4 - - - +
315P TRP* 3.6 29.2 - - + -
316P TYR* 3.5 4.5 - - - -
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Residues in contact with VAL 245 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156P THR* 3.9 26.2 - - + +
159P CYS* 3.2 31.9 - - + +
160P LEU* 4.9 13.5 - - + +
163P VAL* 5.9 1.1 - - + -
178P MET* 4.4 8.7 - - - -
179P THR 3.6 3.8 - - - +
180P THR* 4.0 4.9 - - - +
244P VAL* 1.3 74.6 - - - +
246P ASP* 1.3 62.3 + - - +
247P LEU* 3.8 4.5 - - + +
312P VAL 3.5 1.7 - - - +
313P ILE* 3.3 8.4 - - - +
314P ALA* 3.0 39.2 + - + +
316P TYR* 3.7 19.7 - - + +
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Residues in contact with ASP 246 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179O THR* 2.4 37.2 + - + +
235O LEU* 5.8 5.8 - - + -
246O ASP* 4.4 9.1 - - - +
178P MET* 3.1 6.7 - - - -
179P THR* 2.8 40.6 + - + +
244P VAL* 4.0 1.3 + - + +
245P VAL* 1.3 71.1 - - - +
247P LEU* 1.3 59.9 + - - +
248P VAL* 3.9 5.4 + - - +
311P LYS* 3.1 28.7 + - - +
312P VAL 3.8 2.5 - - - -
313P ILE* 3.4 16.2 - - + +
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Residues in contact with LEU 247 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160P LEU* 3.8 28.0 - - + -
163P VAL* 4.2 14.4 - - + -
164P ALA* 4.6 11.4 - - + -
167P LEU* 4.2 24.5 - - + -
173P ILE* 6.2 0.4 - - + -
177P THR 3.3 18.6 - - - +
178P MET* 3.9 11.2 - - + -
230P LEU* 4.4 11.2 - - + -
245P VAL* 3.8 5.1 - - + -
246P ASP* 1.3 72.6 + - - +
248P VAL* 1.3 60.5 + - - +
249P VAL* 3.4 24.2 - - + -
310P VAL 3.4 1.2 - - - +
311P LYS* 3.1 5.5 - - - +
312P VAL* 2.9 45.6 + - + +
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Residues in contact with VAL 248 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177O THR* 3.5 34.8 - - + -
248O VAL* 3.9 21.5 - - + -
309O LEU* 5.4 1.9 - - + +
311O LYS* 6.1 0.4 - - - +
176P GLY* 3.1 2.4 - - - -
177P THR* 2.8 49.7 + - + +
246P ASP* 3.9 6.0 + - - +
247P LEU* 1.3 76.3 - - - +
249P VAL* 1.3 64.5 + - - +
309P LEU* 3.8 25.8 - - + -
310P VAL 3.2 3.6 - - - +
311P LYS* 3.7 20.4 - - + +
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Residues in contact with VAL 249 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167P LEU* 4.0 8.7 - - + -
173P ILE* 3.8 30.1 - - + -
175P LYS 3.6 7.0 - - - +
176P GLY* 3.8 10.5 - - - -
230P LEU* 4.2 8.3 - - + -
247P LEU* 3.4 28.0 - - + -
248P VAL* 1.3 80.4 - - - +
250P GLN* 1.3 60.2 + - - +
251P VAL* 3.9 3.1 - - + -
308P ASP 3.4 0.7 - - - +
309P LEU* 3.5 5.3 - - - -
310P VAL* 2.7 72.0 + - + +
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Residues in contact with GLN 250 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250O GLN* 2.6 29.2 - - - +
308O ASP* 5.0 0.7 - - - +
309O LEU* 5.5 5.7 - - + +
173P ILE* 3.9 1.7 - - - -
174P ILE* 3.1 53.9 + - + +
175P LYS* 2.6 55.2 + - + +
176P GLY* 4.7 0.2 - - - -
249P VAL* 1.3 72.2 - - - +
251P VAL* 1.3 65.0 + - - +
308P ASP* 3.1 21.6 - - - +
309P LEU* 4.0 12.9 - - + +
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Residues in contact with VAL 251 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167P LEU* 5.5 0.4 - - + -
171P PHE* 3.7 24.2 - - + -
172P GLY 3.1 11.4 - - - +
173P ILE* 4.2 8.7 - - + -
174P ILE* 3.5 13.5 - - - +
249P VAL* 3.9 21.1 - - + -
250P GLN* 1.3 79.2 - - - +
252P GLU* 1.3 64.4 + - - +
253P LYS 3.5 21.5 - - - +
255P THR* 4.6 1.6 - - + -
307P GLY 4.5 1.1 - - - +
308P ASP* 2.8 43.7 + - - +
310P VAL* 4.0 17.7 - - + -
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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