Contacts of the strand formed by residues 267 - 275 (chain A) in PDB entry 4ND1
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 ALA 267 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260A ALA* 4.1 9.2 - - + -
265A LYS* 3.2 23.5 - - + -
266A LYS* 1.3 77.6 - - - +
268A VAL* 1.3 63.8 + - - +
269A VAL* 3.4 17.2 + - + +
291A THR 3.2 4.3 - - - +
292A ILE* 3.3 2.2 - - - -
293A ILE 3.0 26.9 + - - -
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Residues in contact with VAL 268 (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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190A ASN* 5.3 6.3 - - - +
266A LYS 5.0 2.0 - - - +
267A ALA* 1.3 70.8 - - - +
269A VAL* 1.3 63.9 + - - +
270A PRO* 3.8 9.1 - - + +
290A PRO* 4.4 15.0 - - + -
291A THR 3.2 8.3 - - - +
292A ILE* 3.9 18.4 - - + -
303A LEU* 4.1 20.6 - - + -
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Residues in contact with VAL 269 (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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166A VAL* 3.6 25.4 - - + -
256A LYS 5.7 1.3 - - - +
257A MET* 3.8 15.5 - - + -
260A ALA* 4.4 7.4 - - + -
267A ALA* 3.6 25.1 - - + +
268A VAL* 1.3 79.0 - - - +
270A PRO* 1.3 68.1 - - - +
271A CYS* 3.2 5.7 + - + -
290A PRO* 4.3 0.4 - - - -
291A THR* 2.6 41.8 + - - +
293A ILE* 3.6 34.1 - - + -
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Residues in contact with PRO 270 (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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164A ALA 5.0 0.2 + - - -
165A GLY* 3.2 28.6 + - - +
166A VAL* 3.1 35.0 + - + +
169A SER* 3.7 16.2 - - - +
190A ASN* 4.1 18.2 - - + +
191A VAL 4.1 9.6 - - - +
192A ILE* 5.8 0.2 - - + -
268A VAL* 3.8 11.7 - - + +
269A VAL* 1.3 81.6 - - - +
271A CYS* 1.3 59.5 + - - +
289A VAL 3.3 13.0 - - - +
290A PRO* 4.0 7.1 - - + -
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Residues in contact with CYS 271 (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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161A CYS* 4.1 17.9 - - - -
162A GLY 3.3 13.5 - - - +
163A MET* 5.0 0.2 - - - -
165A GLY* 4.3 8.1 - - - +
257A MET* 3.6 26.2 - - + -
269A VAL* 3.2 3.9 + - + +
270A PRO* 1.3 75.4 - - - +
272A SER* 1.3 61.4 + - - +
273A ALA* 3.2 9.3 + - - -
288A GLY* 3.9 5.6 - - - -
289A VAL* 3.0 30.1 + - - +
291A THR* 3.7 28.0 - - - -
293A ILE* 4.2 6.3 - - - -
298A VAL* 4.6 1.6 - - - -
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Residues in contact with SER 272 (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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142A LEU* 3.4 28.7 - - - -
143A ASP* 2.8 28.5 + - - -
146A VAL* 4.4 2.7 - - - +
161A CYS* 3.2 10.5 - - - +
162A GLY 2.9 37.2 + - - -
164A ALA* 5.1 2.5 - - - +
271A CYS* 1.3 68.9 - - - +
273A ALA* 1.3 57.6 + - - +
286A TYR* 3.6 12.4 - - - +
287A MET 3.4 17.5 + - - -
288A GLY* 4.1 1.5 - - - +
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Residues in contact with ALA 273 (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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160A VAL 5.1 0.4 - - - -
161A CYS* 4.7 0.9 - - - -
271A CYS* 3.2 3.5 + - - +
272A SER* 1.3 74.8 - - - +
274A PHE* 1.3 61.5 + - - +
275A CYS* 3.0 11.4 + - - +
285A ILE 3.3 0.2 - - - +
286A TYR* 3.4 9.6 - - - -
287A MET 3.1 25.3 + - - +
289A VAL* 4.2 6.5 - - + +
291A THR* 3.8 29.2 - - + -
298A VAL* 4.1 23.6 - - + -
302A ILE* 4.7 3.8 - - + -
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Residues in contact with PHE 274 (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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157A HIS* 3.3 58.1 + + + +
273A ALA* 1.3 69.1 - - - +
275A CYS* 1.3 60.0 + - - +
276A SER* 3.7 17.4 + - - -
282A LYS 5.2 0.2 - - - -
283A GLY* 3.4 38.1 - - - -
285A ILE* 3.6 9.4 - - - -
286A TYR* 3.4 30.4 - + + -
298A VAL* 5.9 0.2 - - - +
302A ILE* 3.8 10.4 - - - +
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Residues in contact with CYS 275 (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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273A ALA 3.0 5.7 + - - +
274A PHE* 1.3 70.3 - - - +
276A SER* 1.3 59.4 + - - +
278A HIS* 3.4 45.1 - - - -
279A TYR* 4.0 12.6 - - - -
281A VAL* 3.5 16.2 - - + +
283A GLY* 3.2 4.6 + - - -
285A ILE 2.8 34.9 + - - +
287A MET* 4.3 9.9 - - + -
289A VAL* 4.3 7.2 - - + -
302A ILE* 3.8 18.2 - - + -
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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