Contacts of the strand formed by residues 315 - 322 (chain A) 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 THR 315 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258A LYS* 3.3 4.7 - - - +
259A PHE 2.8 36.0 + - - +
261A TYR* 3.8 35.8 + - + -
313A THR* 2.9 20.2 + - - -
314A GLU* 1.3 75.0 + - - +
316A LEU* 1.3 66.8 + - - +
317A LEU* 3.2 11.8 - - + +
401A VAL* 4.5 9.4 - - + -
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Residues in contact with LEU 316 (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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256A GLU* 3.7 28.5 - - + +
257A SER* 3.4 24.7 - - - +
258A LYS* 4.3 15.6 - - + +
315A THR* 1.3 72.1 - - - +
317A LEU* 1.3 69.6 + - - +
400A ARG* 3.2 32.8 + - + +
401A VAL* 3.7 20.6 + - - +
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Residues in contact with LEU 317 (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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256A GLU* 3.5 4.0 - - - +
257A SER 2.7 32.1 + - - +
259A PHE* 3.9 17.3 - - + +
261A TYR* 3.6 46.0 - - + -
271A LEU* 4.8 3.6 - - + -
315A THR* 3.2 23.6 - - + +
316A LEU* 1.3 82.6 - - - +
318A VAL* 1.3 60.9 + - - +
319A VAL* 3.5 24.9 - - + -
401A VAL* 3.5 23.3 - - + -
402A THR 4.4 1.1 - - - +
403A PHE* 3.9 16.2 - - + -
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Residues in contact with VAL 318 (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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254A TYR* 3.3 31.6 - - + +
255A GLN 3.6 5.8 - - - -
256A GLU* 4.3 8.1 - - - +
317A LEU* 1.3 74.0 - - - +
319A VAL* 1.3 57.2 + - - +
320A HIS* 4.0 6.9 + - + +
400A ARG* 3.4 47.1 - - - +
402A THR* 3.1 42.5 - - + +
403A PHE 3.2 20.1 + - - +
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Residues in contact with VAL 319 (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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230A PHE* 4.5 8.0 - - + -
253A MET 3.8 0.3 - - - +
254A TYR* 3.2 7.5 - - - -
255A GLN* 2.9 37.6 + - + +
259A PHE* 4.2 17.5 - - + -
271A LEU* 3.9 25.8 - - + -
273A LEU* 4.7 1.6 - - + -
317A LEU* 3.5 27.1 - - + -
318A VAL* 1.3 69.1 - - - +
320A HIS* 1.3 69.6 + - - +
321A MET* 3.9 28.5 - - + -
403A PHE* 3.7 9.4 - - + -
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Residues in contact with HIS 320 (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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236A ARG* 2.9 37.7 + - - -
238A GLU* 3.5 12.6 + - - -
252A MET* 3.4 16.2 - - + -
253A MET 3.2 4.0 - - - -
254A TYR* 3.6 20.4 - + + -
318A VAL* 4.5 11.0 + - + +
319A VAL* 1.3 75.8 - - - +
321A MET* 1.3 62.1 + - - +
400A ARG* 5.9 1.1 - - - -
402A THR* 4.9 3.7 - - + +
403A PHE* 3.0 8.8 + - - +
404A LYS* 3.2 54.9 + - + +
405A ALA* 3.2 20.4 + - - +
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Residues in contact with MET 321 (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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226A TRP* 4.9 3.1 - - + -
230A PHE* 3.7 16.8 - - + -
252A MET* 3.0 5.6 - - - -
253A MET* 2.7 47.8 + - + +
273A LEU* 3.5 40.6 - - + -
282A MET* 5.0 1.6 - - - +
284A LEU* 3.6 28.3 - - + -
319A VAL* 3.9 12.1 - - + -
320A HIS* 1.3 73.3 - - - +
322A PRO* 1.4 77.0 - - + +
324A PHE* 5.0 4.9 - - + -
376A VAL* 4.2 17.9 - - + -
403A PHE* 6.0 0.2 - - + -
405A ALA* 4.2 2.0 - - + -
409A PHE* 5.1 1.8 - - + -
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Residues in contact with PRO 322 (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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240A PHE* 4.1 18.8 - - + -
250A VAL* 4.1 28.5 - - + -
251A LEU 3.6 6.7 - - - +
252A MET* 3.4 6.9 - - + -
253A MET* 4.3 0.6 - - - +
321A MET* 1.4 95.2 - - + +
323A ARG* 1.3 61.9 + - - +
324A PHE* 3.2 35.6 - - + -
376A VAL* 4.2 2.4 - - - +
405A ALA 3.2 20.0 - - - +
409A PHE* 4.1 9.9 - - + -
430A PRO* 4.2 9.9 - - + -
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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