Contacts of the strand formed by residues 356 - 360 (chain A) in PDB entry 5IXC
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 TYR 356 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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286A LEU* 4.2 2.8 - - - +
290A GLU* 2.6 29.4 + - - -
293A PHE* 5.3 0.2 - + - -
294A LEU* 3.5 28.3 - - + +
322A VAL* 3.7 31.6 - - + -
323A VAL 3.1 3.6 + - - -
324A GLY* 3.3 4.6 - - - -
325A ILE 2.7 31.2 + - - -
354A VAL* 3.3 8.4 - - - +
355A THR* 1.3 88.4 - - + +
357A PHE* 1.3 58.0 + - - +
358A SER 4.1 0.2 - - - -
458A PRO* 4.1 0.7 - - - -
459A LEU* 3.6 22.0 - - + -
461A LEU* 3.9 16.6 - - + -
659A MET* 3.8 17.7 - - + -
664A ARG* 3.4 31.9 + - + +
666A LEU* 4.1 13.2 - - + -
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Residues in contact with PHE 357 (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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325A ILE* 3.7 34.1 - - + -
327A ALA* 5.2 1.1 - - + -
338A LEU* 3.9 24.0 - - + -
342A LEU* 3.9 32.5 - - + -
356A TYR* 1.3 74.0 - - - +
358A SER* 1.3 64.1 + - - +
367A MET* 3.3 34.9 - - + +
370A LEU* 5.0 1.1 - - + -
371A TYR* 3.9 25.8 - + - +
376A TRP* 4.2 12.8 - + - -
458A PRO* 4.0 14.6 - - + +
459A LEU 2.7 13.5 + - - +
460A PRO* 3.2 3.4 - - + +
461A LEU* 2.6 33.1 + - - +
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Residues in contact with SER 358 (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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325A ILE 2.9 23.4 + - - +
326A MET* 3.6 2.6 - - - -
327A ALA* 3.1 22.0 + - - +
357A PHE* 1.3 80.5 - - - +
359A GLY* 1.3 59.0 + - - +
367A MET* 4.1 3.1 - - - -
461A LEU* 3.2 19.3 - - - -
655A SER* 2.5 34.1 + - - -
658A SER* 4.1 5.2 - - - -
659A MET* 3.6 18.5 - - - +
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Residues in contact with GLY 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A ALA* 3.6 10.3 - - - -
358A SER* 1.3 75.3 - - - +
360A ILE* 1.3 64.8 + - - +
363A SER* 4.0 8.7 - - - -
364A THR* 3.8 9.1 - - - +
367A MET* 3.5 17.1 - - - -
461A LEU 3.1 6.4 + - - +
463A LEU* 3.1 26.9 + - - +
655A SER* 3.7 1.8 - - - -
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Residues in contact with ILE 360 (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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327A ALA 3.4 9.9 + - - +
329A GLY* 3.5 18.6 - - - +
359A GLY* 1.3 77.4 - - - +
361A SER* 1.3 83.5 + - - +
362A GLY 3.2 1.0 + - - -
363A SER* 3.1 17.1 + - - -
364A THR* 3.9 3.1 - - - -
463A LEU* 4.0 20.6 - - + +
480A TRP* 3.9 26.0 - - + -
527A TRP 5.1 1.3 - - - +
650A TYR 5.3 7.9 - - - +
653A ASN* 4.0 10.5 - - + +
654A THR* 3.4 31.4 - - - +
655A SER* 4.1 9.0 - - - +
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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