Contacts of the strand formed by residues 260 - 265 (chain B) in PDB entry 1ATT
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 ARG 260 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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259B PHE* 1.3 79.2 - - - +
261B TYR* 1.3 59.1 + - - +
271B LEU* 3.9 0.9 - - - -
272B GLU* 2.9 60.2 + - + +
274B PRO* 3.2 44.9 - - - +
278B ASP* 5.4 1.6 + - - +
281B THR* 3.6 1.8 + - - -
308B TRP* 5.5 0.6 - - - -
311B GLU* 2.9 35.7 - - + +
312B LEU* 4.8 4.3 - - - +
313B THR 3.0 16.2 - - - +
314B GLU* 4.5 2.9 - - + +
416B VAL* 5.1 12.7 - - - +
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Residues in contact with TYR 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B ARG* 1.3 77.9 - - - +
262B ARG* 1.3 79.5 + - - +
263B ARG* 2.9 55.0 + - + +
269B GLN* 4.1 26.1 + - + -
270B VAL 3.1 18.4 - - - -
271B LEU* 4.7 3.6 - - - -
311B GLU* 3.8 5.3 - - - +
313B THR* 3.3 16.1 + - - +
315B THR* 3.6 27.8 - - + +
317B LEU* 3.7 27.4 - - + -
401B VAL* 4.1 23.6 - - + -
402B THR 6.6 0.2 - - - -
403B PHE* 5.0 4.9 - + - -
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Residues in contact with ARG 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B TYR* 1.3 87.0 - - - +
263B ARG* 1.3 62.9 + - - +
264B VAL* 3.8 14.6 - - + +
268B THR 3.4 2.8 - - - +
269B GLN* 3.6 1.9 - - - -
270B VAL* 2.9 47.8 + - + +
306B GLN* 3.3 26.5 + - - +
307B GLU* 3.2 24.3 + - - +
310B ASP* 3.1 56.4 + - - +
311B GLU* 4.1 2.0 - - - -
313B THR* 5.3 1.8 - - - +
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Residues in contact with ARG 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261B TYR* 2.9 38.4 + - + +
262B ARG* 1.3 74.1 + - - +
264B VAL* 1.3 62.3 + - - +
267B SER* 3.4 40.8 - - - +
268B THR 3.4 4.5 - - - +
269B GLN* 4.8 6.6 + - + +
401B VAL* 3.7 33.1 + - - +
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Residues in contact with VAL 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B ARG* 3.8 36.1 - - + +
263B ARG* 1.3 79.9 - - - +
265B ALA* 1.3 66.2 + - + +
267B SER* 2.9 22.3 + - - -
268B THR* 3.0 39.4 + - + +
270B VAL* 3.9 4.7 - - + -
307B GLU* 3.6 37.9 - - + +
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Residues in contact with ALA 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264B VAL* 1.3 74.4 - - + +
266B GLU* 1.3 69.1 + - + +
267B SER 2.9 8.8 + - - -
268B THR* 3.2 16.3 + - - -
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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