Contacts of the helix formed by residues 646 - 659 (chain A) in PDB entry 1QFM
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 PRO 646 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A PRO* 5.8 8.1 - - + -
202A THR* 6.2 0.9 - - + -
637A THR* 3.5 30.7 - - + +
638A ALA 3.8 17.5 - - - +
639A ASP* 4.6 12.6 - - - +
641A ASP 3.3 15.0 - - - +
644A VAL 3.2 1.9 - - - +
645A VAL* 1.4 80.9 - - + +
647A LEU* 1.3 66.3 + - - +
648A HIS 2.9 4.3 + - - -
649A SER* 2.9 16.6 + - - +
650A LEU* 3.0 23.4 + - + +
674A VAL* 5.4 2.7 - - + -
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Residues in contact with LEU 647 (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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31A LEU 3.6 20.6 - - - +
32A GLU* 3.8 36.6 - - + +
202A THR* 4.1 8.7 - - + -
582A ASP* 5.3 3.4 - - + +
589A TYR* 3.9 35.7 - - + -
645A VAL* 3.0 25.0 + - + -
646A PRO* 1.3 79.8 - - - +
648A HIS* 1.3 76.5 + - + +
650A LEU* 3.7 13.3 - - - +
651A LYS* 2.9 38.3 + - + +
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Residues in contact with HIS 648 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579A GLY 3.3 18.2 - - - +
580A VAL* 3.9 7.4 - - + +
581A MET* 3.2 16.2 + - - +
582A ASP* 3.0 49.9 + - + +
585A LYS 5.0 0.7 - - - -
586A PHE* 3.8 25.2 + - + +
589A TYR* 4.6 2.4 - + - -
595A TRP* 4.8 4.8 - - - -
617A LEU* 5.6 0.5 - - - +
644A VAL* 3.7 14.9 - - + +
645A VAL* 3.2 39.9 + - + +
646A PRO 2.9 0.2 + - - -
647A LEU* 1.3 86.9 - - + +
649A SER* 1.3 63.0 + - - +
651A LYS* 4.1 2.7 - - - +
652A PHE* 3.2 24.9 + - - +
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Residues in contact with SER 649 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576A ALA 5.3 0.9 + - - -
578A VAL* 4.9 0.3 - - - -
579A GLY 4.3 17.8 + - - -
581A MET* 4.5 5.7 - - - +
635A LEU* 3.6 22.7 - - - +
636A LEU 4.6 1.7 + - - -
637A THR* 3.9 21.0 - - - -
646A PRO* 2.9 8.4 + - - +
648A HIS* 1.3 75.8 - - - +
650A LEU* 1.3 67.0 + - - +
652A PHE* 4.3 1.3 - - - -
653A ILE* 2.9 27.4 + - - +
672A ILE* 3.8 18.6 - - - -
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Residues in contact with LEU 650 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LEU* 3.9 24.7 - - + +
34A PRO* 6.3 0.4 - - + -
39A THR* 3.8 28.9 - - + -
42A PHE* 3.5 27.5 - - + -
43A VAL* 4.0 13.5 - - + -
637A THR* 5.0 1.8 - - + -
646A PRO* 3.0 26.1 + - + +
647A LEU* 3.8 11.2 - - - +
649A SER* 1.3 77.2 - - - +
651A LYS* 1.3 62.5 + - - +
653A ILE* 3.4 5.5 - - - +
654A ALA* 3.1 19.4 + - - +
672A ILE* 3.9 18.8 - - + -
674A VAL* 4.0 16.6 - - + -
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Residues in contact with LYS 651 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ASP* 2.7 34.2 + - - -
28A TYR* 3.5 34.1 - - + +
31A LEU* 4.1 13.0 - - + -
32A GLU* 2.7 38.2 + - + +
582A ASP* 2.9 23.5 + - + +
585A LYS* 4.0 0.4 - - - +
617A LEU* 3.7 18.8 - - + -
647A LEU* 2.9 27.8 + - + +
648A HIS* 4.2 2.7 - - - +
650A LEU* 1.3 75.0 - - - +
652A PHE* 1.3 62.0 + - - +
654A ALA* 3.5 2.1 + - - +
655A THR* 2.8 29.6 + - - -
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Residues in contact with PHE 652 (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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561A ALA* 3.6 32.1 - - + -
565A ASN* 4.4 7.4 - - - -
581A MET* 3.8 21.1 - - + -
616A PRO* 3.3 36.6 - - + -
617A LEU* 3.9 12.2 - - + +
620A VAL* 3.6 17.5 - - + -
633A MET* 4.1 12.1 - - + -
635A LEU* 3.7 22.7 - - + -
648A HIS 3.2 20.4 + - - +
649A SER 3.8 3.1 - - - +
650A LEU 3.3 0.2 - - - -
651A LYS* 1.3 76.5 - - - +
653A ILE* 1.3 56.5 + - - +
655A THR* 3.2 2.1 + - - -
656A LEU* 2.9 54.3 + - + +
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Residues in contact with ILE 653 (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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42A PHE* 3.7 17.3 - - + -
46A GLN* 4.5 2.9 - - - -
633A MET* 5.9 0.9 - - + -
635A LEU* 3.8 12.0 - - + +
649A SER 2.9 16.0 + - - +
650A LEU 3.4 11.4 - - - +
652A PHE* 1.3 75.6 - - - +
654A ALA* 1.3 67.4 + - - +
656A LEU* 3.7 18.1 - - + +
657A GLN* 2.9 41.1 + - - +
670A LEU* 3.6 26.2 - - + +
671A LEU 3.7 17.9 - - - +
672A ILE* 3.9 27.6 - - + -
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Residues in contact with ALA 654 (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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9A VAL* 4.3 5.9 - - + +
28A TYR* 3.7 33.0 + - + -
31A LEU* 4.3 2.0 - - + -
42A PHE* 4.0 20.6 - - + -
650A LEU 3.1 13.5 + - - +
651A LYS 3.7 4.9 - - - +
652A PHE 3.3 0.2 - - - -
653A ILE* 1.3 82.6 - - - +
655A THR* 1.3 58.0 + - - +
657A GLN* 3.9 6.6 - - - +
658A TYR* 3.0 29.8 + - - +
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Residues in contact with THR 655 (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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11A ARG* 6.2 0.9 - - - +
28A TYR* 3.5 19.6 - - + -
617A LEU* 3.3 26.3 - - + +
620A VAL* 3.8 26.9 - - + -
651A LYS 2.8 21.6 + - - -
652A PHE 3.5 4.3 - - - -
654A ALA* 1.3 75.2 - - - +
656A LEU* 1.3 59.0 + - - +
658A TYR* 4.7 1.8 - - - -
659A ILE* 2.9 42.7 + - + +
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Residues in contact with LEU 656 (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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620A VAL* 4.0 20.4 - - + -
630A TYR* 3.9 29.8 - - + -
633A MET* 4.1 24.0 - - + -
635A LEU* 4.6 2.7 - - + -
652A PHE* 2.9 52.8 + - + +
653A ILE* 3.7 24.2 - - + +
655A THR* 1.3 76.2 - - - +
657A GLN* 1.3 57.3 + - - +
660A VAL* 2.9 16.3 + - + +
661A GLY 2.8 21.5 + - - -
670A LEU* 3.7 13.8 - - + +
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Residues in contact with GLN 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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6A TYR* 3.3 43.3 - - + +
7A PRO* 3.8 8.8 - - - +
9A VAL* 5.1 1.9 - - - +
46A GLN* 3.0 41.9 + - - +
49A ILE* 4.5 2.0 - - - +
653A ILE* 2.9 28.7 + - + +
654A ALA* 3.9 4.6 - - - +
656A LEU* 1.3 75.3 - - - +
658A TYR* 1.3 58.3 + - - +
661A GLY* 3.1 8.3 - - - +
662A ARG* 3.1 30.7 + - - +
670A LEU* 3.0 29.2 + - + +
671A LEU* 4.5 1.6 - - - +
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Residues in contact with TYR 658 (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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9A VAL 5.9 1.6 - - - -
11A ARG* 3.3 51.1 + - + -
13A GLU* 4.7 3.1 + - - -
28A TYR* 3.2 18.6 - - + +
654A ALA 3.0 11.8 + - - +
655A THR* 4.0 2.2 - - - +
657A GLN* 1.3 77.0 - - - +
659A ILE* 1.3 81.7 + - + +
662A ARG* 3.2 76.7 + - - +
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Residues in contact with ILE 659 (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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11A ARG* 5.3 4.9 - - - +
620A VAL* 3.8 32.3 - - + +
621A LYS* 4.3 6.5 - - - -
622A LEU* 3.5 24.1 - - + +
655A THR* 2.9 35.6 + - + +
658A TYR* 1.3 95.9 - - + +
660A VAL* 1.3 62.9 + - + +
662A ARG* 5.3 0.5 - - - +
663A SER* 4.7 3.6 + - - -
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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