Contacts of the strand formed by residues 266 - 271 (chain C) in PDB entry 1NDD
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 VAL 266 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204C LYS* 3.4 24.2 - - + +
206C LYS* 3.9 36.1 - - + +
212C GLU* 5.2 1.3 - - - +
244C ILE 4.3 1.6 - - - +
245C TYR* 3.5 19.0 - - - -
264C GLY 3.6 9.4 + - - +
265C SER* 1.3 76.3 - - - +
267C LEU* 1.3 63.9 + - - +
268C HIS* 4.0 22.6 + - + +
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Residues in contact with LEU 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203C ILE* 3.7 26.7 - - + -
204C LYS 2.7 17.0 + - - +
205C VAL* 3.3 10.1 - - + +
206C LYS 2.9 25.5 + - - -
226C ILE* 4.3 7.0 - - + -
243C LEU* 4.3 20.9 - - + -
244C ILE 3.6 4.9 - - - +
245C TYR* 3.8 24.0 - - + -
250C MET* 3.9 25.1 - - + -
261C ILE* 3.6 32.1 - - + -
265C SER* 4.8 2.0 - - - -
266C VAL* 1.3 74.4 - - - +
268C HIS* 1.3 62.0 + - - +
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Residues in contact with HIS 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206C LYS* 3.4 19.6 + - + +
207C THR 5.1 2.0 + - - -
208C LEU* 4.7 11.4 - - + +
242C ARG 3.3 5.2 - - - +
243C LEU* 3.3 3.4 - - - -
244C ILE* 2.8 57.3 + - + +
245C TYR* 5.8 0.4 - - - -
246C SER 6.0 0.2 - - - -
266C VAL* 4.3 23.8 + - + +
267C LEU* 1.3 72.3 - - - +
269C LEU* 1.3 59.6 + - - +
270C VAL* 4.0 4.7 + - + -
306D LYS* 6.4 2.0 - - - -
307D THR 4.8 3.7 + - - -
308D LEU* 3.9 45.7 + - + -
310D GLY* 5.6 2.8 + - - -
368D HIS* 5.0 15.5 - + - -
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Residues in contact with LEU 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B LEU* 3.8 23.3 - - + +
173B LEU* 4.6 12.3 - - + -
205C VAL* 3.6 27.8 - - + -
206C LYS 3.0 12.0 + - - +
207C THR* 3.6 23.2 - - + +
208C LEU 4.3 1.2 + - - -
230C VAL* 4.1 17.5 - - + -
236C ILE* 4.1 10.5 - - + -
241C GLN* 3.7 35.4 - - + +
242C ARG 3.4 10.8 - - - +
243C LEU* 3.8 13.0 - - + -
267C LEU 3.7 0.4 + - - -
268C HIS* 1.3 72.4 - - - +
270C VAL* 1.3 68.0 + - - +
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Residues in contact with VAL 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A LEU* 4.5 8.7 - - + -
108B LEU* 5.4 6.3 - - + -
109B THR* 4.3 15.9 - - + -
171B LEU* 4.3 4.7 - - - -
2001B CL 3.8 7.4 - - + -
208C LEU* 4.2 28.7 - - + -
240C GLN 4.0 0.2 - - - +
241C GLN* 3.9 2.1 - - - -
242C ARG* 3.0 64.2 + - + +
244C ILE* 4.3 16.6 - - + -
268C HIS* 5.0 5.2 - - + -
269C LEU* 1.3 81.8 - - - +
271C LEU* 1.3 61.8 + - - +
308D LEU* 5.7 1.3 - - + -
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Residues in contact with LEU 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B THR* 4.4 14.8 + - + -
108B LEU* 5.8 0.9 - - - +
109B THR* 3.4 26.5 + - - +
136B ILE* 3.5 33.9 - - + -
169B LEU* 3.6 37.0 - - + +
171B LEU* 3.7 33.1 - - + +
2001B CL 3.3 16.6 - - + +
236C ILE* 4.7 2.0 - - + -
240C GLN* 3.6 14.6 - - + +
270C VAL* 1.3 74.2 - - - +
272C ALA* 1.3 59.1 + - - +
273C LEU* 3.8 20.9 - - + -
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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