Contacts of the strand formed by residues 663 - 675 (chain A) in PDB entry 3HIG
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 663 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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525A THR 3.3 0.2 - - - +
526A LYS* 3.7 14.8 + - - -
527A ASN 2.8 27.9 + - - +
626A LYS* 2.7 42.1 + - + -
659A ASN* 3.4 28.3 - - - +
660A ILE* 4.1 2.0 - - - -
661A GLU 3.4 12.4 - - - +
662A ASN* 1.3 82.8 - - - +
664A ASP* 1.3 63.2 + - - +
665A LEU* 3.3 23.1 + - + +
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Residues in contact with ASP 664 (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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79A LYS* 2.7 29.9 + - - +
519A ASP* 3.5 1.4 - - - +
525A THR* 3.1 29.7 - - + +
526A LYS* 3.8 10.9 - - + +
626A LYS* 3.7 7.1 - - + +
627A TYR* 2.8 50.0 + - + +
663A GLU* 1.3 73.2 + - - +
665A LEU* 1.3 57.3 + - - +
802A CA 2.3 31.9 - - - -
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Residues in contact with LEU 665 (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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519A ASP* 3.2 4.5 - - - +
520A LEU* 3.3 8.7 + - - +
525A THR 4.4 0.6 + - - -
527A ASN* 3.8 15.4 - - + +
528A SER* 3.7 33.2 - - - +
529A PHE* 3.9 7.4 - - + +
579A PHE* 4.4 12.1 - - + -
624A VAL* 4.0 18.6 - - + -
625A THR 3.4 7.2 - - - +
626A LYS* 4.8 0.4 - - - -
660A ILE* 3.6 41.1 - - + +
663A GLU* 3.3 20.9 + - + +
664A ASP* 1.3 78.8 + - - +
666A VAL* 1.3 62.4 + - - +
802A CA 2.3 30.4 - - - -
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Residues in contact with VAL 666 (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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517A ARG* 3.8 40.4 - - + +
518A VAL 3.9 9.0 - - - +
519A ASP* 3.9 9.9 - - - +
624A VAL* 3.3 7.5 - - - -
625A THR* 2.8 42.1 + - - +
627A TYR* 4.0 25.1 - - + -
665A LEU* 1.3 80.3 - - - +
667A ALA* 1.3 69.5 + - - +
668A TRP* 3.6 23.9 - - + +
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Residues in contact with ALA 667 (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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518A VAL* 2.8 52.0 + - + +
520A LEU* 4.9 3.6 - - + +
579A PHE* 3.7 32.6 - - + -
595A LEU* 4.8 6.3 - - + -
622A LEU* 4.1 9.9 - - + -
623A ALA 3.5 4.7 - - - -
624A VAL* 4.6 2.0 - - - +
666A VAL* 1.3 76.5 - - - +
668A TRP* 1.3 61.0 + - - +
669A VAL* 4.2 1.1 - - + -
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Residues in contact with TRP 668 (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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353A GLN* 4.1 2.5 - - + -
515A HIS* 3.5 32.6 + + + +
516A TYR 3.4 3.8 - - - -
517A ARG* 3.1 60.1 - - + -
620A TYR* 4.7 1.4 - - - +
621A PRO 3.7 0.7 - - - +
622A LEU* 3.3 6.9 - - - +
623A ALA* 2.8 39.9 + - + +
625A THR* 2.8 30.6 + - + +
631A GLU* 3.6 13.9 - - + -
632A LEU 4.0 4.5 - - - -
633A CYS 4.1 1.3 - - - -
634A SER* 3.7 28.3 - - - -
650A PHE* 3.5 24.7 - + + -
653A PHE* 4.0 12.8 - + - -
666A VAL* 3.6 16.8 - - + +
667A ALA* 1.3 74.7 - - - +
669A VAL* 1.3 62.0 + - - +
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Residues in contact with VAL 669 (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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514A VAL 3.6 1.4 - - - +
515A HIS* 3.2 8.2 + - - -
516A TYR* 2.8 45.7 + - + +
518A VAL* 4.1 18.2 - - + -
595A LEU* 3.9 31.2 - - + -
597A ILE* 4.1 16.4 - - + -
621A PRO 3.3 10.8 - - - +
622A LEU* 4.4 2.5 - - + -
667A ALA* 4.8 0.9 - - + -
668A TRP* 1.3 78.4 - - - +
670A THR* 1.3 62.0 + - - +
671A VAL* 3.9 23.7 + - + -
694A PHE* 4.1 12.1 - - + -
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Residues in contact with THR 670 (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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513A LEU* 4.2 17.0 - - + -
514A VAL 3.4 8.3 - - - +
515A HIS* 3.2 12.5 - - - -
569A PHE* 4.0 19.6 - - + -
597A ILE* 4.5 3.5 - - - +
599A SER* 4.1 4.9 + - - -
601A ALA* 4.6 0.2 - - + -
617A TRP* 3.0 25.9 + - + -
618A ALA* 4.3 6.7 - - - -
620A TYR 2.9 25.9 + - - -
621A PRO* 3.0 22.3 + - - +
669A VAL* 1.3 72.5 - - - +
671A VAL* 1.3 73.1 + - - +
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Residues in contact with VAL 671 (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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479A MET* 6.1 0.2 - - + -
513A LEU* 3.5 2.4 - - - -
514A VAL* 2.7 46.4 + - + +
516A TYR* 4.1 22.2 - - + -
597A ILE* 4.0 10.3 - - + -
599A SER* 3.3 11.0 - - - +
601A ALA* 4.1 3.8 - - - -
669A VAL* 3.9 17.9 + - + -
670A THR* 1.3 81.6 - - - +
672A GLY* 1.3 56.6 + - - +
692A VAL* 3.7 26.0 - - + -
693A GLY* 3.5 29.6 - - - +
694A PHE* 4.8 1.8 - - + -
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Residues in contact with GLY 672 (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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479A MET* 6.4 0.2 - - - -
512A HIS* 3.1 14.4 - - - -
514A VAL* 4.8 0.7 - - - -
599A SER* 3.0 7.1 + - - -
600A MET 2.8 28.6 + - - -
601A ALA* 3.0 12.9 + - - +
671A VAL* 1.3 78.2 - - - +
673A PHE* 1.3 66.5 + - - +
692A VAL* 3.6 12.5 - - - +
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Residues in contact with PHE 673 (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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479A MET* 4.4 15.7 - - + -
481A ALA* 4.2 17.9 - - + -
511A THR* 3.5 6.2 - - - +
512A HIS* 2.9 66.8 + + + -
600A MET* 4.1 23.6 - - + -
601A ALA* 4.5 1.0 - - - +
672A GLY* 1.3 80.0 - - - +
674A LEU* 1.3 75.3 + - - +
675A HIS* 3.6 12.2 + + + -
685A THR* 6.3 0.4 - - + -
690A ASN* 3.8 38.8 - - - -
692A VAL* 3.9 18.2 - - + -
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Residues in contact with LEU 674 (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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509A ILE* 3.8 22.0 - - + -
510A HIS 3.4 18.4 - - - +
511A THR* 3.6 17.9 - - + +
600A MET* 4.4 6.6 + - - +
673A PHE* 1.3 82.6 - - - +
675A HIS* 1.3 58.1 + - - +
676A ILE* 4.0 15.5 - - + -
533B GLN* 4.5 3.1 - - - -
534B MET* 3.9 33.9 - - + +
575B LYS* 4.4 21.8 - - + -
576B TYR* 3.1 38.7 + - + -
594B ARG* 4.8 4.5 + - - -
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Residues in contact with HIS 675 (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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461A TPQ 3.5 7.0 - - - -
485A VAL* 4.0 6.3 - - + -
509A ILE* 3.8 0.5 - - - +
510A HIS* 2.8 46.7 + + - +
512A HIS* 3.7 10.2 + - + -
673A PHE* 3.6 12.8 + + + -
674A LEU* 1.3 73.2 - - - +
676A ILE* 1.3 75.6 - - - +
677A PRO* 3.4 10.1 - - + +
678A HIS* 4.8 4.4 + + - -
681A ASP* 2.9 25.2 + - - -
685A THR* 3.5 30.2 - - + +
690A ASN* 5.7 3.3 + - - -
801A CU 2.0 33.9 - - - -
576B TYR* 3.5 4.0 - - - -
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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