Contacts of the helix formed by residues 669 - 687 (chain D) in PDB entry 1S77
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 669 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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609D VAL* 6.1 2.8 - - - +
667D PHE* 3.0 14.6 - - - +
668D THR* 1.3 77.2 + - - +
670D PRO* 1.3 65.3 - - - +
671D ASN* 2.5 44.2 - - + +
672D GLN* 2.7 32.5 + - - +
673D ALA* 3.9 0.9 - - - +
19N G 3.7 30.5 + - - +
20N T 6.0 2.6 - - - +
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Residues in contact with PRO 670 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651D LEU* 3.3 25.8 - - + -
655D ILE* 3.4 23.1 - - + +
656D GLN* 5.9 0.2 - - - -
659D ILE* 4.0 16.2 - - + -
667D PHE* 4.8 3.9 - - + -
669D GLN* 1.3 78.3 - - - +
671D ASN* 1.3 77.3 + - - +
673D ALA* 3.1 8.0 - - + +
674D ALA* 2.8 24.6 + - - +
19N G 3.2 28.5 - - + +
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Residues in contact with ASN 671 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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647D ARG* 2.6 38.6 - - - +
651D LEU* 4.8 7.1 - - - +
669D GLN* 2.5 40.1 - - - +
670D PRO* 1.3 85.5 - - - +
672D GLN* 1.3 62.7 + - + +
673D ALA 2.4 16.5 + - - -
674D ALA* 3.7 7.9 - - - +
675D GLY 5.0 0.2 - - - +
19N G 3.5 31.9 + - - +
20N T 4.2 16.8 + - - +
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Residues in contact with GLN 672 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609D VAL* 5.5 1.2 + - - +
610D LYS* 3.3 22.5 - - + +
611D LEU* 3.0 40.6 + - + +
616D LEU* 4.2 16.2 - - + -
668D THR 4.7 3.0 + - - -
669D GLN* 2.7 41.4 - - - +
671D ASN* 1.3 75.8 - - + +
673D ALA* 1.3 56.3 + - - +
674D ALA 3.0 2.3 - - - +
675D GLY* 3.7 9.2 - - - +
676D TYR* 2.6 40.0 + - - +
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Residues in contact with ALA 673 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616D LEU* 4.2 10.0 - - + +
619D GLN* 4.4 5.2 - - - +
620D TRP* 2.7 35.6 + - - +
655D ILE* 3.9 3.8 - - + -
667D PHE* 3.6 35.7 - - + +
669D GLN 3.9 7.6 + - - +
670D PRO 3.1 13.9 - - - +
671D ASN 2.4 20.7 + - - +
672D GLN* 1.3 69.4 - - - +
674D ALA* 1.3 53.8 + - - +
676D TYR* 3.8 0.6 - - - +
677D MET 3.2 10.4 + - - -
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Residues in contact with ALA 674 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647D ARG* 3.9 15.5 - - + +
650D VAL* 3.5 25.2 - - + +
651D LEU* 4.0 14.4 - - + -
655D ILE* 3.8 9.9 - - + -
670D PRO 2.8 17.9 + - - +
671D ASN* 4.3 3.4 - - - -
673D ALA* 1.3 74.5 - - - +
675D GLY* 1.3 54.7 + - - +
676D TYR 3.1 1.6 - - - -
677D MET* 3.0 3.2 + - - +
678D ALA* 2.6 37.8 + - - +
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Residues in contact with GLY 675 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643D GLU* 4.7 2.4 - - - +
647D ARG* 4.0 14.8 - - - +
672D GLN* 3.2 12.7 + - - +
674D ALA* 1.3 78.1 - - - +
676D TYR* 1.3 61.3 + - - +
678D ALA* 3.4 9.5 + - - +
679D LYS* 3.1 22.7 + - - +
21N T 6.5 1.3 - - - -
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Residues in contact with TYR 676 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582D LEU* 3.4 27.4 - - + +
585D ASP* 2.9 23.0 + - - +
613D THR* 3.2 27.2 - - + +
616D LEU* 3.4 26.9 - - + -
617D ALA* 3.2 30.8 - - + +
620D TRP* 3.6 20.4 - + - -
672D GLN* 2.6 24.2 + - - +
673D ALA 3.8 1.6 - - - +
675D GLY* 1.3 71.0 - - - +
677D MET* 1.3 65.3 + - - +
679D LYS* 3.0 16.9 + - + +
680D LEU* 3.2 37.1 + - + +
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Residues in contact with MET 677 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578D VAL* 4.0 15.0 - - + -
582D LEU* 4.2 11.7 - - + -
620D TRP* 3.2 51.4 - - + +
625D VAL* 3.6 18.6 - - + -
629D VAL* 4.2 7.2 - - + -
630D THR* 5.7 0.2 - - - -
650D VAL* 3.6 23.1 - - + -
673D ALA 3.2 16.4 + - - +
674D ALA 3.0 5.0 + - - +
676D TYR* 1.3 80.6 - - - +
678D ALA* 1.3 63.7 + - - +
679D LYS 3.2 0.2 + - - -
680D LEU* 3.2 5.6 + - + -
681D ILE* 3.0 49.1 + - + +
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Residues in contact with ALA 678 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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643D GLU* 3.6 16.5 - - + +
646D PHE* 3.6 15.2 - - + +
647D ARG* 3.4 35.0 - - + +
650D VAL* 4.6 1.3 - - - +
674D ALA 2.6 19.8 + - - +
675D GLY* 3.4 7.2 - - - +
677D MET* 1.3 73.7 - - - +
679D LYS* 1.3 56.9 - - - +
681D ILE* 3.7 3.5 + - - -
682D TRP* 3.1 26.5 + - - +
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Residues in contact with LYS 679 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643D GLU* 3.5 29.1 + - - +
675D GLY 3.1 10.0 + - - +
676D TYR* 3.0 13.8 + - + +
678D ALA* 1.3 75.2 - - - +
680D LEU* 1.3 70.0 + - + +
681D ILE 3.2 0.2 - - - -
682D TRP* 3.3 0.5 + - - +
683D GLU* 3.0 54.3 + - + +
22N G 5.8 2.9 + - - +
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Residues in contact with LEU 680 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578D VAL* 4.1 19.1 - - + -
581D ILE* 3.3 44.2 - - + +
582D LEU* 3.4 36.8 - - + -
585D ASP* 4.6 1.3 - - - +
676D TYR* 3.2 37.6 + - + +
677D MET* 3.2 8.9 + - - +
679D LYS* 1.3 80.9 - - + +
681D ILE* 1.3 56.1 + - - +
683D GLU* 3.5 8.3 + - - +
684D SER* 2.7 37.5 + - - -
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Residues in contact with ILE 681 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574D VAL* 4.5 8.5 - - + +
578D VAL* 4.1 7.9 - - + -
629D VAL 3.9 21.1 - - - +
630D THR* 4.0 22.2 - - + +
633D SER* 3.5 32.8 - - - +
634D VAL 5.0 0.2 - - - +
646D PHE* 3.8 7.0 - - + -
650D VAL* 5.1 5.2 - - + -
677D MET* 3.0 43.9 + - + +
678D ALA* 3.9 6.7 - - - +
680D LEU* 1.3 77.4 - - - +
682D TRP* 1.3 53.1 + - - +
684D SER* 3.9 1.3 - - - -
685D VAL* 2.6 45.0 + - + +
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Residues in contact with TRP 682 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637D LEU* 4.0 15.7 - - + -
641D SER 3.7 7.9 - - - -
642D LYS* 3.3 33.7 - - + -
643D GLU* 3.2 57.6 + - + +
646D PHE* 3.7 17.0 - + + -
678D ALA 3.1 19.1 + - - +
679D LYS 3.6 4.3 - - - +
680D LEU 3.2 0.2 - - - -
681D ILE* 1.3 76.5 - - - +
683D GLU* 1.3 68.2 + - + +
685D VAL* 3.3 6.4 - - - +
686D SER* 2.6 53.7 + - - -
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Residues in contact with GLU 683 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581D ILE* 4.6 8.9 - - + +
643D GLU* 5.6 0.2 - - - +
679D LYS* 3.0 52.3 + - + +
680D LEU* 4.0 13.0 - - - +
682D TRP* 1.3 86.5 - - + +
684D SER* 1.3 58.2 + - - +
686D SER* 4.1 3.8 - - - -
687D VAL* 3.1 29.6 + - - +
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Residues in contact with SER 684 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574D VAL* 4.2 7.2 - - - -
577D LYS* 3.7 28.5 - - - +
578D VAL* 3.7 15.3 + - - +
581D ILE* 3.5 18.2 - - - +
680D LEU 2.7 23.3 + - - -
681D ILE 3.9 2.2 - - - -
683D GLU* 1.3 75.5 - - - +
685D VAL* 1.3 61.7 + - - +
686D SER 3.2 1.1 - - - -
687D VAL* 2.9 27.7 - - - +
688D THR* 3.1 9.5 + - - -
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Residues in contact with VAL 685 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574D VAL* 4.1 11.9 - - + +
633D SER 4.3 1.1 - - - +
634D VAL* 3.6 44.4 - - + -
637D LEU* 3.9 26.9 - - + -
646D PHE* 3.9 15.5 - - + -
681D ILE* 2.6 32.7 + - + +
682D TRP* 3.3 13.0 - - - +
684D SER* 1.3 74.4 - - - +
686D SER* 1.3 61.9 + - - +
688D THR* 3.2 2.3 + - - -
689D VAL* 3.0 30.9 + - + +
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Residues in contact with SER 686 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637D LEU* 4.9 6.3 - - - +
682D TRP* 2.6 49.1 + - - -
683D GLU* 4.1 6.7 - - - -
685D VAL* 1.3 77.8 - - - +
687D VAL* 1.3 57.8 + - - +
688D THR 2.8 11.2 + - - -
689D VAL 3.6 7.6 - - - +
690D VAL* 3.5 19.4 - - - +
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Residues in contact with VAL 687 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577D LYS* 3.6 27.5 - - + -
683D GLU 3.1 17.0 - - - +
684D SER* 2.9 23.3 - - - +
686D SER* 1.3 75.1 - - - +
688D THR* 1.3 55.8 + - - +
690D VAL* 4.7 5.6 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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