Contacts of the helix formed by residues 489 - 506 (chain B) in PDB entry 1B70
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 GLU 489 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A ARG* 2.7 47.0 + - - +
119A TYR 3.9 0.2 - - - +
120A GLN* 3.4 27.8 + - - +
121A ALA* 3.3 41.7 + - + +
487B GLY 2.5 8.4 + - - +
488B VAL* 1.3 74.5 - - - +
490B ALA* 1.3 65.8 + - - +
491B PRO* 3.4 0.7 - - - -
492B TYR* 3.1 6.9 + - + +
493B ARG* 2.9 46.3 + - + +
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Residues in contact with ALA 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487B GLY* 3.0 14.5 + - - +
489B GLU* 1.3 76.3 - - - +
491B PRO* 1.3 62.1 - - + +
493B ARG* 3.0 7.3 + - - +
494B LYS* 2.6 36.8 + - - +
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Residues in contact with PRO 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A VAL* 6.3 0.9 - - + -
488B VAL 3.2 17.0 - - - +
489B GLU 3.5 0.7 - - - -
490B ALA* 1.3 95.4 - - + +
492B TYR* 1.3 62.2 + - - +
494B LYS* 3.2 7.8 + - + +
495B GLU* 3.0 22.9 + - - +
676B PRO* 6.6 0.2 - - + -
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Residues in contact with TYR 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A GLU* 2.8 41.6 + - - +
108A ARG* 5.2 1.9 + - - -
111A VAL* 3.8 13.4 - - + +
115A ARG* 4.0 18.4 - - - -
121A ALA* 3.5 38.1 - - + +
122A VAL* 4.8 2.5 - - - +
123A GLU* 3.7 36.3 - - + -
199A PRO* 3.9 19.0 - - + +
488B VAL 5.6 0.2 - - - +
489B GLU* 3.1 8.6 + - + +
491B PRO* 1.3 78.8 - - - +
493B ARG* 1.3 66.3 + - - +
495B GLU* 3.2 8.7 + - - +
496B GLN* 3.0 52.9 + - + +
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Residues in contact with ARG 493 (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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112A GLU* 5.2 3.6 + - - -
115A ARG* 2.9 57.9 - - - +
489B GLU* 2.9 38.0 + - + +
490B ALA* 3.2 11.9 - - - +
492B TYR* 1.3 79.1 - - - +
494B LYS* 1.3 65.1 + - - +
496B GLN* 3.0 8.0 + - - +
497B ARG* 3.0 32.7 + - + +
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Residues in contact with LYS 494 (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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490B ALA 2.6 17.2 + - - +
491B PRO* 3.3 13.2 - - + +
493B ARG* 1.3 75.1 - - - +
495B GLU* 1.3 64.1 + - - +
497B ARG* 3.2 10.4 + - + +
498B LEU* 3.2 34.6 + - - +
620B LEU* 4.7 15.5 - - - +
622B LEU* 6.3 1.3 - - - -
676B PRO* 5.2 15.0 - - + -
677B LEU* 5.1 23.6 - - - +
679B ASP* 4.9 14.8 - - + +
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Residues in contact with GLU 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A GLU* 3.6 23.1 - - - +
491B PRO 3.0 12.7 + - - +
492B TYR* 3.4 11.2 - - - +
494B LYS* 1.3 77.7 - - - +
496B GLN* 1.3 70.9 + - - +
498B LEU* 3.4 11.3 - - + +
499B ARG* 2.9 42.3 + - - +
573B VAL* 4.5 19.0 - - + +
575B ARG* 4.4 6.7 + - - -
583B THR* 3.7 20.1 + - + +
675B LEU* 5.4 5.0 - - + +
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Residues in contact with GLN 496 (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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104A THR* 4.0 16.0 + - - +
107A GLU* 4.0 2.4 + - - +
108A ARG* 5.9 5.5 - - - +
115A ARG* 6.1 0.4 - - - +
492B TYR* 3.0 48.8 + - + +
493B ARG* 3.0 10.7 + - - +
495B GLU* 1.3 82.6 - - - +
497B ARG* 1.3 66.7 + - - +
498B LEU 3.1 1.1 - - - -
499B ARG* 3.1 43.2 + - - +
500B GLU* 2.8 39.2 + - - +
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Residues in contact with ARG 497 (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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493B ARG* 3.0 20.4 + - + +
494B LYS* 3.7 16.6 - - - +
496B GLN* 1.3 73.4 - - - +
498B LEU* 1.3 60.4 + - - +
500B GLU* 3.0 35.2 + - - +
501B VAL* 2.8 39.1 + - + +
620B LEU* 6.6 0.2 - - + -
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Residues in contact with LEU 498 (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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494B LYS* 3.2 25.9 + - - +
495B GLU* 3.4 15.3 - - + +
497B ARG* 1.3 79.8 - - - +
499B ARG* 1.3 64.8 + - - +
500B GLU 3.1 0.9 + - - -
501B VAL* 3.1 7.2 + - + +
502B LEU* 3.1 44.1 + - + +
573B VAL* 5.9 4.0 - - + -
585B LEU* 4.4 10.8 - - + -
616B LEU* 4.2 17.9 - - + -
620B LEU* 4.7 8.3 - - + -
675B LEU* 3.9 30.1 - - + -
677B LEU* 4.5 15.0 - - + -
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Residues in contact with ARG 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A LEU* 3.9 12.3 - - + +
104A THR* 4.2 11.2 - - + +
107A GLU* 3.9 14.1 + - - -
495B GLU* 2.9 28.0 + - - +
496B GLN* 3.2 43.6 + - - +
498B LEU* 1.3 79.3 - - - +
500B GLU* 1.3 62.7 + - + +
502B LEU* 3.5 12.9 - - - +
503B SER* 3.4 16.5 + - - -
509B GLU* 3.2 33.0 + - - +
511B TYR* 3.6 25.2 + - - -
571B PHE* 4.0 8.5 - - + -
573B VAL* 4.0 39.2 + - - +
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Residues in contact with GLU 500 (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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100A LEU* 4.4 9.5 - - + +
108A ARG* 2.9 46.5 + - - +
496B GLN* 2.8 24.0 + - - +
497B ARG* 3.1 44.2 + - - +
499B ARG* 1.3 74.7 - - + +
501B VAL* 1.3 64.3 - - - +
503B SER* 2.5 24.1 + - - +
504B GLY* 3.0 7.4 + - - -
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Residues in contact with VAL 501 (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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497B ARG* 2.8 31.2 + - + +
498B LEU* 3.6 8.7 - - - +
500B GLU* 1.3 71.5 - - + +
502B LEU* 1.3 53.1 + - - +
504B GLY* 2.9 5.5 + - - -
505B LEU* 2.7 39.1 + - + +
616B LEU* 4.4 16.4 - - + -
619B ARG* 3.6 39.0 - - + +
620B LEU* 4.4 12.3 - - + -
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Residues in contact with LEU 502 (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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498B LEU* 3.1 36.7 + - + +
499B ARG* 3.5 6.3 - - - +
501B VAL* 1.3 75.3 - - - +
503B SER* 1.3 56.0 + - - +
505B LEU* 2.6 29.7 + - + +
506B GLY 3.0 9.4 + - - -
507B PHE* 3.3 31.6 + - + -
571B PHE* 3.5 40.2 - - + -
573B VAL* 5.2 1.1 - - + -
585B LEU* 4.3 15.3 - - + -
616B LEU* 4.2 29.2 - - + -
671B PHE* 6.1 3.8 - - + -
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Residues in contact with SER 503 (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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98A GLY* 3.2 26.6 + - - +
99A GLY* 3.5 25.4 - - - -
100A LEU* 3.7 23.4 - - - +
499B ARG 3.4 1.6 + - - -
500B GLU* 2.5 32.2 + - - +
502B LEU* 1.3 78.3 - - - +
504B GLY* 1.3 59.8 + - - +
506B GLY 3.5 1.4 + - - -
507B PHE 3.5 14.1 + - - -
571B PHE* 4.7 0.8 - - - -
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Residues in contact with GLY 504 (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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500B GLU 3.0 9.3 + - - -
501B VAL* 2.9 9.7 + - - -
503B SER* 1.3 75.2 + - - +
505B LEU* 1.3 62.5 + - - +
506B GLY* 4.7 0.2 - - - -
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Residues in contact with LEU 505 (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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96A PHE 3.9 4.1 - - - +
501B VAL* 2.7 14.2 + - + +
502B LEU* 2.6 20.7 + - + +
504B GLY* 1.3 74.5 - - - +
506B GLY* 1.3 53.9 - - - -
507B PHE* 4.1 16.4 - - + -
612B TYR* 3.4 36.3 + - + +
615B ALA* 4.6 10.8 - - + -
616B LEU* 4.0 40.8 - - + +
619B ARG* 6.3 0.7 - - + -
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Residues in contact with GLY 506 (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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96A PHE* 3.0 42.3 - - - +
97A SER 4.0 1.0 - - - -
98A GLY* 3.2 19.5 + - - -
502B LEU 3.0 0.6 + - - -
503B SER 3.5 1.2 + - - -
504B GLY 3.3 2.8 - - - -
505B LEU* 1.3 80.2 - - - +
507B PHE* 1.3 65.3 + - - +
508B GLN 4.0 0.5 + - - -
569B LEU* 3.6 10.6 - - - +
612B TYR* 4.7 0.7 - - - -
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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