Contacts of the strand formed by residues 377 - 386 (chain B) in PDB entry 1EOB
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 377 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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364B ILE* 3.8 34.2 - - + +
372B LEU* 4.5 18.7 - - - +
375B GLY 3.4 8.6 + - - +
376B GLU* 1.3 70.2 - - - +
378B VAL* 1.3 59.3 + - - +
440B ARG* 3.8 22.4 - - - +
441B THR 3.8 6.3 - - - -
442B ILE* 4.3 5.8 - - + -
517B ASP* 2.8 44.6 + - - +
518B SER* 3.5 14.5 + - - +
519B ARG* 3.1 23.0 + - - +
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Residues in contact with VAL 378 (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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364B ILE* 4.9 0.8 - - - +
376B GLU 3.1 7.8 + - - +
377B ARG* 1.3 79.4 - - - +
379B ILE* 1.3 63.4 + - - +
380B VAL* 4.7 8.3 - - + -
440B ARG* 3.7 3.3 - - - +
441B THR* 2.9 58.5 + - + +
443B LYS* 3.9 23.6 - - + +
480B PHE* 5.0 6.5 - - + -
518B SER* 4.5 0.4 - - - -
519B ARG* 3.4 37.5 - - + +
521B TYR* 4.4 16.4 - - + -
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Residues in contact with ILE 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B VAL* 1.3 79.0 - - - +
380B VAL* 1.3 68.1 + - - +
381B HIS* 4.2 2.2 - - + -
438B VAL* 3.9 20.6 - - + -
439B PHE 3.6 10.8 - - - +
440B ARG* 4.2 19.5 - - + -
512B ASN 5.5 2.7 - - - +
514B ILE* 3.5 33.2 - - + -
518B SER* 4.2 13.9 - - - +
519B ARG 2.8 14.2 + - - +
520B CYS* 3.2 15.5 - - + -
521B TYR* 2.8 26.9 + - - +
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Residues in contact with VAL 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B VAL* 4.2 14.3 + - + -
379B ILE* 1.3 79.7 - - - +
381B HIS* 1.3 64.7 + - - +
437B TYR* 3.8 13.7 - - - +
438B VAL* 3.4 2.3 - - - +
439B PHE* 2.9 69.9 + - + +
441B THR* 4.8 1.3 - - + -
461B ILE* 4.8 5.2 - - + -
478B PHE* 3.8 25.8 - - + -
480B PHE* 4.8 3.6 - - + -
521B TYR* 3.5 20.2 - - + +
523B PHE* 4.6 5.8 - - + -
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Residues in contact with HIS 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B ILE* 5.0 1.5 - - + +
380B VAL* 1.3 75.3 - - - +
382B GLY* 1.3 59.8 + - - +
436B TYR* 2.8 31.1 + + - +
437B TYR* 3.2 26.5 + - - +
438B VAL* 3.9 9.4 - - + -
509B ASP* 2.8 28.5 + - - -
512B ASN* 3.9 16.6 - - + -
520B CYS* 3.3 18.7 - - - -
521B TYR 3.1 17.2 + - - -
522B ARG* 3.4 10.2 - - - -
523B PHE 2.9 23.0 + - - -
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Residues in contact with GLY 382 (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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381B HIS* 1.3 80.3 - - - +
383B TYR* 1.3 66.3 + - - -
436B TYR* 3.3 9.0 - - - -
437B TYR* 3.0 34.7 + - - -
522B ARG* 3.7 10.3 - - - -
523B PHE 3.5 6.5 - - - -
524B ASP* 3.2 11.9 - - - -
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Residues in contact with TYR 383 (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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382B GLY* 1.3 75.7 - - - -
384B VAL* 1.3 64.1 + - - +
385B ARG* 3.9 29.1 + - + +
434B ASN* 3.5 30.5 - - + +
435B GLY 3.4 3.4 - - - -
436B TYR* 3.6 39.9 - + + -
437B TYR* 4.0 0.8 - - - -
522B ARG* 3.2 33.9 - - - -
523B PHE 4.5 0.2 - - - +
524B ASP* 2.6 16.8 + - - +
525B ILE 2.9 26.0 + - - +
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Residues in contact with VAL 384 (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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383B TYR* 1.3 76.7 - - - +
385B ARG* 1.3 62.9 + - - +
391B PRO* 3.6 4.5 - - - +
392B VAL* 2.9 45.0 + - + +
395B ALA* 5.2 0.9 - - + -
397B VAL* 4.8 2.0 - - + -
431B THR* 3.6 28.3 - - + -
434B ASN 4.7 0.3 - - - +
435B GLY* 2.7 17.0 + - - +
437B TYR* 4.0 14.4 - - + -
465B LEU* 3.7 28.7 - - + -
525B ILE* 3.3 20.2 - - + +
527B LEU* 4.0 8.5 - - + -
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Residues in contact with ARG 385 (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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5A LEU* 4.7 22.0 - - + +
383B TYR* 3.9 24.8 + - + +
384B VAL* 1.3 77.9 - - - +
386B ASP* 1.3 68.2 + - - +
389B GLY* 3.8 23.6 - - - +
390B ARG 3.2 11.9 - - - +
391B PRO* 4.8 3.8 - - + -
392B VAL* 3.6 8.9 - - - +
434B ASN 5.9 0.7 - - - +
522B ARG* 3.9 9.1 - - - +
524B ASP* 3.1 38.3 + - - +
525B ILE 2.9 7.6 + - - +
526B THR* 3.3 5.3 + - - +
527B LEU* 2.7 24.6 + - - +
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Residues in contact with ASP 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU* 4.9 1.2 - - - +
385B ARG* 1.3 78.0 - - - +
387B GLN* 1.3 59.4 + - - +
388B PHE* 2.8 15.4 + - - -
389B GLY* 2.8 16.1 + - - -
390B ARG* 2.8 66.5 + - - +
391B PRO 5.3 0.5 - - - +
392B VAL* 3.8 9.1 - - + +
472B GLN* 4.8 2.7 - - - +
526B THR* 4.0 4.0 - - - +
527B LEU 3.1 8.1 - - - -
528B ARG 3.6 18.4 - - - +
529B GLY* 3.7 6.2 - - - -
530B ARG 4.9 0.2 + - - -
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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