Contacts of the strand formed by residues 241 - 249 (chain P) in PDB entry 3K9Q
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 241 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206O ILE* 4.3 2.0 - - - -
177P ILE 3.4 11.9 - - - -
178P HIS* 3.4 9.4 + - - -
179P ALA 3.0 17.3 + - - -
240P GLY* 1.3 68.9 - - - -
242P LEU* 1.3 61.6 + - - +
283P VAL* 4.7 1.4 - - - +
313P TRP* 3.3 13.6 - - - -
314P TYR* 2.7 62.4 + - - -
316P ASN* 2.8 21.0 + - - -
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Residues in contact with LEU 242 (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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206O ILE* 4.8 2.9 - - + -
233O GLN* 3.3 40.6 - - - +
175P THR 4.0 0.3 - - - +
176P THR* 2.9 5.4 + - - -
177P ILE* 2.9 43.9 + - + +
241P SER* 1.3 75.7 - - - +
243P THR* 1.3 65.2 + - - +
244P GLU* 4.3 10.3 - - + +
296P GLN* 3.7 24.2 - - - +
311P ALA* 4.0 6.5 - - + -
312P ALA 3.5 20.0 - - - +
313P TRP* 3.5 37.5 - - + +
314P TYR* 4.0 0.2 - - - -
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Residues in contact with THR 243 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152P THR* 3.9 1.9 - - - +
155P SER* 2.7 29.9 + - - +
156P LEU* 4.5 17.9 - - + -
174P MET* 3.8 30.3 - - + -
175P THR 3.8 2.5 - - - -
176P THR* 3.5 8.5 + - - -
242P LEU* 1.3 72.1 - - - +
244P GLU* 1.3 64.3 + - - +
245P LEU* 4.2 3.2 + - + +
310P VAL 3.8 0.2 - - - +
311P ALA* 2.9 6.8 - - - +
312P ALA* 2.8 40.2 + - + -
314P TYR* 3.1 12.6 + - - -
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Residues in contact with GLU 244 (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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175O THR* 2.5 40.7 + - - +
233O GLN* 2.9 27.4 + - - -
173P LEU 4.0 0.6 - - - +
174P MET* 3.2 5.2 - - - +
175P THR* 2.8 47.1 + - - +
177P ILE* 4.0 17.6 - - + +
242P LEU* 4.3 3.4 - - + -
243P THR* 1.3 75.8 - - - +
245P LEU* 1.3 59.5 + - - +
246P THR* 5.2 1.6 - - - +
296P GLN* 5.4 0.5 - - - -
309P LYS* 4.0 17.5 - - - +
310P VAL 3.3 6.5 - - - +
311P ALA* 4.2 12.7 - - + +
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Residues in contact with LEU 245 (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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156P LEU* 3.7 30.1 - - + -
159P VAL* 4.1 10.1 - - + -
160P ALA* 4.6 7.4 - - + -
163P LEU* 3.7 27.6 - - + -
173P LEU 3.6 13.7 - - - +
174P MET* 4.0 17.3 - - + -
228P LEU* 4.0 24.7 - - + -
243P THR* 4.1 4.2 - - + +
244P GLU* 1.3 73.8 - - - +
246P THR* 1.3 60.4 + - - +
247P VAL* 3.5 12.7 - - + +
308P VAL 3.6 1.2 - - - +
309P LYS* 3.2 4.3 - - - +
310P VAL* 2.9 42.4 + - + +
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Residues in contact with THR 246 (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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173O LEU* 4.2 27.1 - - + +
246O THR* 4.1 30.8 + - + -
307O LEU* 3.9 4.5 - - + +
172P GLY* 3.2 1.7 - - - -
173P LEU 2.8 38.1 + - - -
244P GLU* 5.2 1.2 - - - +
245P LEU* 1.3 74.9 + - - +
247P VAL* 1.3 61.1 + - - +
307P LEU* 4.4 15.3 - - + -
308P VAL 3.3 4.3 - - - +
309P LYS* 3.6 22.1 - - - +
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Residues in contact with VAL 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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307O LEU* 4.9 0.7 - - - -
163P LEU* 4.0 13.5 - - + -
169P LEU* 3.9 19.5 - - + -
171P GLU 3.4 7.9 - - - +
172P GLY* 4.0 5.8 - - - -
228P LEU* 4.6 0.9 - - + -
245P LEU* 3.5 33.9 - - + -
246P THR* 1.3 81.1 - - - +
248P VAL* 1.3 61.8 + - - +
249P LEU* 3.7 22.4 - - + -
306P GLN 4.2 0.2 - - - +
307P LEU* 3.4 9.9 - - - +
308P VAL* 2.7 56.9 + - + +
310P VAL* 6.3 0.2 - - + -
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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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248O VAL* 4.9 4.5 - - + -
305O ARG* 3.5 30.1 - - - +
307O LEU* 3.7 29.8 - - + -
169P LEU* 3.9 0.9 - - - +
170P VAL* 2.8 42.6 + - + +
171P GLU* 2.8 27.3 + - + +
247P VAL* 1.3 71.9 - - - +
249P LEU* 1.3 69.3 + - - +
306P GLN 4.4 10.1 - - - +
307P LEU* 3.7 12.8 - - + -
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Residues in contact with LEU 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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305O ARG* 5.0 2.8 + - - -
163P LEU* 4.3 15.0 - - + +
167P PHE* 3.7 35.7 - - + +
168P GLY 3.2 11.7 - - - +
169P LEU* 4.2 12.3 - - + -
170P VAL* 3.7 8.0 - - - +
247P VAL* 3.7 19.5 + - + -
248P VAL* 1.3 87.4 - - - +
250P GLU* 1.3 64.4 + - - +
251P LYS 3.7 13.9 - - - +
252P GLN* 3.7 6.8 - - - +
254P VAL* 4.4 11.4 - - + -
259P VAL* 5.3 0.2 - - + -
306P GLN 5.0 2.6 + - - -
308P VAL* 3.8 33.4 - - + +
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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