Contacts of the helix formed by residues 656 - 675 (chain A) in PDB entry 1HWL
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 GLY 656 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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588A MET* 3.9 5.4 - - - -
651A SER* 3.7 20.2 - - - -
654A ALA* 2.9 9.1 - - - +
655A MET* 1.3 80.4 - - - +
657A MET* 1.3 66.0 + - - +
658A ASN 3.4 2.2 - - - -
659A MET* 3.4 7.3 + - - +
660A ILE* 2.9 27.7 + - - +
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Residues in contact with MET 657 (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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2A FBI 4.5 1.8 - - - -
588A MET* 4.0 8.0 - - + +
589A THR 3.1 28.3 - - - +
590A ARG* 3.6 39.5 - - + +
655A MET* 3.3 35.2 - - + +
656A GLY* 1.3 75.2 - - - +
658A ASN* 1.3 60.4 + - - +
660A ILE* 3.8 2.9 - - + +
661A SER* 2.9 35.4 + - - -
690A ASP* 3.6 19.1 - - - +
702A ARG* 3.2 18.2 - - - +
770A GLN* 4.1 4.0 - - - +
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Residues in contact with ASN 658 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656A GLY 3.4 0.6 - - - -
657A MET* 1.3 77.9 - - - +
659A MET* 1.3 63.5 + - - +
661A SER* 3.2 7.4 + - - -
662A LYS* 3.0 29.2 + - + +
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Residues in contact with MET 659 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622A PHE* 5.1 0.5 - - - -
625A THR* 4.8 2.1 + - - +
626A SER* 4.0 30.7 - - - +
628A PHE* 4.2 17.0 - - + -
629A ALA* 4.2 14.8 - - + +
650A ARG 4.3 2.2 - - - +
651A SER* 3.6 45.3 - - - +
654A ALA* 4.4 12.8 - - + -
656A GLY* 3.4 8.6 + - - +
657A MET 3.3 0.4 - - - -
658A ASN* 1.3 80.0 - - - +
660A ILE* 1.3 65.8 + - + +
662A LYS* 3.3 10.2 + - - +
663A GLY* 3.0 19.8 + - - -
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Residues in contact with ILE 660 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588A MET* 3.9 20.9 - - + -
589A THR* 4.0 5.4 - - - -
590A ARG* 3.7 32.3 - - + +
622A PHE* 3.8 13.7 - - + -
629A ALA* 6.0 0.2 - - - -
647A PHE* 4.4 6.1 - - + +
649A SER* 3.4 44.9 - - - +
650A ARG 4.3 4.5 - - - +
651A SER* 4.9 3.6 - - - -
656A GLY* 2.9 22.8 + - - +
657A MET* 3.9 4.5 - - + +
659A MET* 1.3 80.0 - - + +
661A SER* 1.3 58.8 + - - +
663A GLY* 3.4 1.2 + - - -
664A THR* 2.8 36.9 + - - +
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Residues in contact with SER 661 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A FBI 4.1 14.8 - - - -
590A ARG* 3.2 33.5 + - - -
657A MET 2.9 22.7 + - - -
658A ASN* 3.5 8.0 - - - -
660A ILE* 1.3 73.6 - - - +
662A LYS* 1.3 66.1 + - - +
664A THR* 3.1 8.2 + - - -
665A GLU* 2.9 33.3 + - - +
683A VAL* 4.9 3.4 - - - -
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Residues in contact with LYS 662 (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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625A THR* 3.7 35.2 + - - +
658A ASN* 3.0 18.2 + - + +
659A MET* 3.6 12.8 - - + +
661A SER* 1.3 75.4 - - - +
663A GLY* 1.3 63.0 + - - +
665A GLU* 3.3 14.0 + - - +
666A LYS* 3.2 22.7 + - - +
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Residues in contact with GLY 663 (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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622A PHE* 3.3 35.9 - - - -
625A THR* 3.6 22.5 + - - -
629A ALA* 5.8 0.2 - - - -
659A MET 3.0 10.6 + - - -
661A SER 3.2 0.2 - - - -
662A LYS* 1.3 81.1 - - - +
664A THR* 1.3 55.2 + - - +
666A LYS* 3.5 0.9 + - - -
667A ALA* 3.0 23.9 + - - +
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Residues in contact with THR 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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590A ARG* 3.7 19.3 - - + +
592A PRO* 3.7 35.0 - - + -
622A PHE* 3.5 5.4 - - - -
647A PHE* 3.7 26.2 - - + +
660A ILE* 2.8 23.1 + - - +
661A SER* 3.1 7.8 + - - -
663A GLY* 1.3 74.8 - - - +
665A GLU* 1.3 60.1 + - - +
667A ALA* 3.3 3.7 + - - +
668A LEU* 2.9 41.7 + - + +
683A VAL* 4.5 5.4 - - + -
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Residues in contact with GLU 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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2A FBI 6.4 1.1 - - - -
661A SER* 2.9 22.7 + - - +
662A LYS* 3.3 14.3 + - - +
664A THR* 1.3 75.5 - - - +
666A LYS* 1.3 61.3 + - - +
668A LEU* 3.2 10.0 + - - +
669A SER* 3.0 23.1 + - - -
683A VAL* 4.0 32.6 - - + +
860B GLY 4.9 8.5 - - - +
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Residues in contact with LYS 666 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621A ALA* 3.5 18.1 - - + +
624A SER* 2.7 36.7 + - - +
625A THR* 3.7 26.0 - - + +
662A LYS 3.2 5.8 + - - +
663A GLY 4.0 1.3 - - - +
665A GLU* 1.3 78.6 - - - +
667A ALA* 1.3 63.5 + - - +
669A SER* 3.1 10.8 + - - -
670A LYS* 3.1 21.5 + - - +
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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
----------------------------------------------------------
618A ILE* 3.7 24.9 - - + +
621A ALA* 4.1 11.4 - - - +
622A PHE* 4.2 5.4 - - + -
647A PHE* 3.6 30.3 - - + -
663A GLY 3.0 18.8 + - - +
664A THR 3.7 1.8 - - - +
666A LYS* 1.3 75.6 - - - +
668A LEU* 1.3 60.1 + - - +
670A LYS* 3.3 3.1 + - - +
671A LEU* 3.0 27.5 + - - +
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Residues in contact with LEU 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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592A PRO* 3.9 25.4 - - + -
594A VAL* 4.2 19.1 - - + -
645A ILE* 4.3 10.5 - - + -
647A PHE* 4.1 22.2 - - + -
664A THR* 2.9 31.4 + - + +
665A GLU* 3.6 8.3 - - - +
666A LYS 3.2 0.2 - - - -
667A ALA* 1.3 75.0 - - - +
669A SER* 1.3 60.0 + - - +
671A LEU* 3.3 12.1 + - + +
672A HIS* 2.9 28.9 + - - +
678A MET* 3.6 4.9 - - + +
680A ILE* 3.7 37.2 - - + +
683A VAL* 5.1 6.3 - - + -
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Residues in contact with SER 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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665A GLU 3.0 14.7 + - - -
666A LYS* 3.1 15.0 + - - -
668A LEU* 1.3 76.3 - - - +
670A LYS* 1.3 63.4 + - - +
672A HIS* 3.0 21.8 + - - +
673A GLU* 3.2 16.9 + - - +
680A ILE* 4.8 3.3 - - - +
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Residues in contact with LYS 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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617A VAL* 3.7 26.5 - - + +
618A ILE* 4.4 4.7 - - + -
621A ALA* 3.8 30.1 - - + -
666A LYS* 3.1 4.8 + - - +
667A ALA 3.6 7.4 - - - +
668A LEU 3.3 0.2 - - - -
669A SER* 1.3 80.0 - - - +
671A LEU* 1.3 62.4 + - - +
673A GLU* 3.0 45.2 + - - +
674A TYR* 3.4 27.4 - - + -
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Residues in contact with LEU 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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605A VAL* 4.2 12.8 - - + -
608A TRP* 3.7 31.2 - - + -
609A LEU* 4.1 11.7 - - + -
618A ILE* 4.0 8.7 - - + +
645A ILE* 4.1 24.5 - - + -
647A PHE* 6.2 0.9 - - + -
667A ALA 3.0 17.4 + - - +
668A LEU* 3.6 11.4 - - + +
670A LYS* 1.3 76.6 - - - +
672A HIS* 1.3 63.6 + - - +
674A TYR* 3.0 9.3 + - + +
675A PHE* 3.0 36.7 + - + +
678A MET* 3.5 27.8 - - + -
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Residues in contact with HIS 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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668A LEU 2.9 13.2 + - - +
669A SER* 3.0 15.8 + - - +
671A LEU* 1.3 77.8 - - - +
673A GLU* 1.3 61.8 + - - +
675A PHE 3.1 7.8 - - - -
676A PRO* 3.0 52.9 + - + +
678A MET* 3.1 35.7 + - + +
680A ILE* 5.2 9.0 - - + -
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Residues in contact with GLU 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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669A SER* 3.2 14.5 + - - +
670A LYS* 3.0 47.6 + - - +
672A HIS* 1.3 79.9 - - + +
674A TYR* 1.3 64.4 + - + +
676A PRO* 4.0 7.8 - - - +
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Residues in contact with TYR 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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608A TRP* 3.6 33.9 - + + -
617A VAL* 3.6 40.8 - - + +
670A LYS* 3.4 25.8 - - + -
671A LEU 3.0 8.2 + - - +
673A GLU* 1.3 84.3 - - + +
675A PHE* 1.3 82.0 + - + +
676A PRO* 3.6 6.1 - - - +
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Residues in contact with PHE 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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596A LEU* 4.7 6.1 - - + -
601A ASP* 5.5 0.4 - - + -
604A GLU* 4.1 30.5 - - + -
605A VAL* 3.6 32.3 - - + -
608A TRP* 3.9 43.5 - + + -
671A LEU* 3.0 26.0 + - + +
672A HIS* 3.1 9.6 - - - +
674A TYR* 1.3 98.2 - - + +
676A PRO* 1.3 61.5 - - - +
677A GLU* 3.2 2.7 - - + -
678A MET* 2.9 35.9 + - + +
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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