Contacts of the strand formed by residues 355 - 361 (chain B) in PDB entry 4H3I
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 GLN 355 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250B TRP* 4.6 8.7 - - + -
350B GLY* 2.7 34.3 + - - -
351B GLU 5.6 0.2 + - - -
352B VAL* 3.1 49.9 + - + +
353B THR 3.1 3.0 - - - +
354B ASN* 1.3 80.2 - - - +
356B SER* 1.3 55.7 + - - +
434B PRO* 3.3 42.3 - - + +
435B PHE 3.5 5.4 - - - +
440B MET* 3.1 9.9 - - - +
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Residues in contact with SER 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B TRP* 5.0 1.1 - - - -
265B VAL* 4.0 15.7 - - - -
347B TYR* 4.0 9.1 - - - -
348B LEU 3.3 16.6 - - - -
350B GLY* 3.8 2.5 - - - +
355B GLN* 1.3 75.3 - - - +
357B PHE* 1.3 65.1 + - - +
434B PRO* 3.4 7.4 - - - +
435B PHE* 2.9 41.0 + - - +
437B THR* 2.7 25.9 + - - -
440B MET* 4.0 4.3 - - - -
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Residues in contact with PHE 357 (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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250B TRP* 3.5 58.6 - + + -
251B TYR 3.3 28.3 - - - -
252B THR* 3.7 14.8 - - - -
347B TYR* 3.2 4.8 - - - +
348B LEU* 2.8 54.1 + - + -
349B MET 3.9 5.2 - - - -
350B GLY* 4.3 4.5 - - - -
356B SER* 1.3 75.4 - - - +
358B ARG* 1.3 70.8 + - - +
359B ILE* 3.9 20.9 - - + -
415B PHE* 4.1 5.8 - + - -
431B VAL* 4.1 6.1 - - + -
432B GLU 3.4 13.5 - - - +
433B GLY* 4.2 0.9 - - - -
435B PHE* 4.0 7.0 - - - -
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Residues in contact with ARG 358 (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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268B GLU* 4.3 7.4 + - - -
345B SER* 4.5 5.8 - - - -
346B LEU 3.3 10.1 - - - +
347B TYR* 2.9 48.5 + - + -
357B PHE* 1.3 77.0 - - - +
359B ILE* 1.3 66.1 + - - +
360B THR* 4.3 12.9 + - - +
430B ALA 3.8 0.3 - - - +
431B VAL* 3.3 5.2 - - - +
432B GLU* 2.8 67.9 + - - +
435B PHE* 3.6 30.4 - - + -
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Residues in contact with ILE 359 (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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344B ILE 3.7 1.2 - - - +
345B SER* 3.2 2.8 - - - -
346B LEU* 2.9 53.6 + - + +
348B LEU* 4.4 7.0 - - + -
357B PHE* 3.9 21.8 - - + -
358B ARG* 1.3 77.9 - - - +
360B THR* 1.3 63.4 + - - +
361B ILE* 4.3 0.7 - - + -
394B MET* 3.5 32.3 - - + -
398B ILE* 4.0 16.8 - - + -
402B PHE* 3.6 20.6 - - + -
415B PHE* 4.0 24.7 - - + -
430B ALA 3.3 4.0 - - - -
431B VAL* 4.3 4.3 - - + -
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Residues in contact with THR 360 (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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343B VAL* 3.7 29.6 - - + -
344B ILE 3.2 6.1 - - - +
345B SER* 2.9 26.6 + - - +
358B ARG* 4.3 13.7 + - - +
359B ILE* 1.3 75.9 - - - +
361B ILE* 1.3 65.5 + - - +
362B LEU* 5.5 0.2 - - + -
402B PHE* 3.5 3.3 - - - -
428B THR 5.3 4.9 - - - +
429B ALA* 3.3 11.1 - - - +
430B ALA* 2.8 43.0 + - - +
432B GLU* 4.6 1.4 + - - -
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Residues in contact with ILE 361 (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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295B LEU* 4.8 7.9 - - + -
343B VAL* 3.4 7.4 - - - +
344B ILE* 2.9 50.1 + - + +
359B ILE* 5.5 0.9 - - + -
360B THR* 1.3 73.2 - - - +
362B LEU* 1.3 65.9 + - - +
365B GLN* 3.8 23.6 - - + +
366B TYR* 4.2 17.4 - - + -
397B VAL* 3.9 22.4 - - + -
398B ILE* 3.8 32.1 - - + +
401B GLY* 5.1 0.7 - - - -
402B PHE* 3.4 32.8 - - + -
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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