Contacts of the strand formed by residues 581 - 590 (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 581 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A PRO* 3.3 17.9 - - + +
126A GLU* 2.5 28.7 + - - +
127A VAL* 2.9 31.5 + - - +
159A PHE* 3.9 11.3 - - + -
160A ARG 4.7 1.4 + - - -
161A LEU* 5.3 1.5 - - + +
575B ARG* 3.1 34.8 - - + -
576B VAL 3.7 4.0 - - - -
577B PHE* 3.5 22.2 - - + -
580B ARG* 1.3 78.5 - - - +
582B GLU* 1.3 63.1 + - - +
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Residues in contact with GLU 582 (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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575B ARG* 3.2 7.2 - - - -
576B VAL* 2.7 49.5 + - + +
578B ARG* 3.9 21.0 + - - +
580B ARG* 4.1 9.7 - - + +
581B GLU* 1.3 80.3 - - - +
583B THR* 1.3 64.9 + - - +
584B HIS* 3.8 13.9 + - + -
674B ARG* 3.1 42.6 + - + -
675B LEU 5.5 1.3 - - - +
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Residues in contact with THR 583 (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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495B GLU* 3.7 19.6 + - - +
573B VAL* 4.0 10.8 - - + -
574B GLY 3.7 7.2 - - - +
575B ARG* 3.3 30.8 + - - +
582B GLU* 1.3 72.2 - - - +
584B HIS* 1.3 57.7 + - - +
674B ARG* 3.6 3.3 - - - +
675B LEU* 2.7 71.2 + - + +
676B PRO* 6.0 0.4 - - - -
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Residues in contact with HIS 584 (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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548B LEU* 3.2 19.1 - - + +
573B VAL* 3.4 7.1 - - - +
574B GLY 2.8 32.6 + - - +
576B VAL* 3.5 26.0 - - + +
578B ARG* 3.5 31.5 - - - -
582B GLU* 3.6 19.3 + - + -
583B THR* 1.3 80.1 - - - +
585B LEU* 1.3 60.7 + - - +
672B GLU* 2.9 29.5 + - + +
673B LEU 3.1 13.9 + - - +
674B ARG* 4.0 14.2 + - + +
675B LEU* 3.7 2.7 - - - -
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Residues in contact with LEU 585 (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* 4.4 18.4 - - + -
502B LEU* 4.3 19.5 - - + -
548B LEU* 4.4 0.4 - - - -
571B PHE* 3.8 17.5 - - + -
572B GLU 3.4 12.8 - - - +
573B VAL* 3.5 17.0 - - + -
584B HIS* 1.3 75.0 - - - +
586B ALA* 1.3 75.0 + - - +
616B LEU* 5.6 5.6 - - + -
671B PHE* 4.4 15.0 - - + -
672B GLU* 3.2 1.0 - - - -
673B LEU* 2.6 49.3 + - + +
675B LEU* 3.7 22.0 - - + -
677B LEU* 6.2 1.8 - - + -
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Residues in contact with ALA 586 (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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548B LEU* 4.0 14.0 - - + +
549B PHE* 4.1 4.9 - - + +
552B LEU* 3.8 14.7 - - + +
571B PHE* 3.2 4.9 - - - +
572B GLU* 3.0 32.8 + - + +
585B LEU* 1.3 77.1 - - - +
587B GLY* 1.3 60.4 + - - +
671B PHE* 3.0 18.6 - - - +
672B GLU* 3.6 25.8 - - + +
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Residues in contact with GLY 587 (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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507B PHE* 5.1 0.7 - - - -
552B LEU* 4.0 4.0 - - - -
570B LEU 3.1 13.7 - - - -
571B PHE* 4.0 2.0 - - - -
586B ALA* 1.3 75.9 - - - +
588B LEU* 1.3 61.0 + - - +
609B LEU* 5.1 0.7 - - - -
669B HIS 3.8 0.2 - - - +
670B LEU* 3.5 6.1 - - - +
671B PHE* 2.9 55.0 + - - +
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Residues in contact with LEU 588 (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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552B LEU* 3.9 16.2 - - + +
553B VAL* 3.6 36.1 - - - +
556B LEU* 3.8 25.6 - - + -
568B ALA* 4.4 7.4 - - + +
569B LEU* 3.4 6.0 - - - +
570B LEU* 2.9 50.6 + - + +
587B GLY* 1.3 74.6 - - - -
589B LEU* 1.3 71.5 + - - +
590B PHE* 4.4 1.3 - - + -
609B LEU* 4.4 0.9 - - - -
668B VAL* 3.5 21.5 - - + -
669B HIS 3.3 3.4 - - - -
670B LEU* 3.7 11.7 - - + -
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Residues in contact with LEU 589 (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* 4.1 23.3 - - + -
568B ALA 3.2 11.4 - - - +
569B LEU* 4.1 10.8 - - + -
588B LEU* 1.3 75.4 - - - +
590B PHE* 1.3 88.5 + - - +
591B GLY 5.8 0.7 - - - +
593B GLY* 5.7 2.7 - - - -
604B SER* 5.5 0.7 - - - -
605B GLY 3.8 22.7 - - - +
608B LEU* 3.5 30.7 - - + -
609B LEU* 3.2 30.9 - - + +
612B TYR* 6.4 0.2 - - + -
668B VAL* 3.3 2.8 - - - +
669B HIS* 2.9 37.7 + - + +
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Residues in contact with PHE 590 (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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556B LEU* 4.0 29.6 - - + -
560B LEU* 3.5 27.1 - - + -
565B PRO* 3.5 24.9 - - + -
566B GLU 3.7 11.9 - - - -
567B ARG* 3.2 7.9 - - - +
568B ALA* 2.7 48.6 + - + +
588B LEU* 4.4 1.1 - - + -
589B LEU* 1.3 89.5 - - - +
591B GLY* 1.3 71.7 + - - +
592B GLU* 5.4 1.1 - - - -
666B PRO* 3.9 25.8 - - + -
667B PRO* 3.9 20.6 - - + +
668B VAL* 4.4 1.3 - - + -
669B HIS* 5.8 1.6 - - - -
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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