Contacts of the helix formed by residues 648 - 659 (chain A) in PDB entry 1MP8
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 648 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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520A LEU* 3.8 30.3 - - + -
524A ILE* 4.2 14.1 - - + -
646A ASN 3.7 5.4 - - - +
647A CYS* 1.3 92.8 - - - +
649A PRO* 1.3 74.0 - - + +
650A THR* 3.9 16.2 - - + +
651A LEU* 3.0 14.5 + - + -
652A TYR* 3.0 17.7 + - - +
679A ILE* 5.0 3.8 - - + -
683A GLU* 4.8 5.4 - - + +
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Residues in contact with PRO 649 (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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643A MET* 4.6 16.6 - - + -
647A CYS 3.4 6.5 - - - +
648A PRO* 1.3 83.5 - - + +
650A THR* 1.3 59.7 + - + +
652A TYR* 3.2 8.4 + - + +
653A SER* 2.7 36.7 + - - -
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Residues in contact with THR 650 (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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648A PRO* 3.9 11.5 - - + +
649A PRO* 1.3 82.2 - - + +
651A LEU* 1.3 59.3 + - - +
653A SER* 3.5 8.5 - - - -
654A LEU* 3.1 23.4 + - - +
679A ILE* 3.9 25.2 - - - +
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Residues in contact with LEU 651 (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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524A ILE* 3.9 21.3 - - + -
527A ALA* 5.5 1.3 - - + -
612A MET* 4.3 14.1 - - - -
616A LEU* 3.8 40.8 - - + -
647A CYS* 3.9 6.3 - - - -
648A PRO* 3.0 16.2 + - + +
650A THR* 1.3 80.4 + - - +
652A TYR* 1.3 65.2 + - - +
654A LEU* 3.1 4.9 + - + +
655A MET* 3.0 24.7 + - + +
676A LEU* 3.6 31.2 - - + -
679A ILE* 3.7 20.6 - - + -
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Residues in contact with TYR 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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640A ARG* 4.4 7.4 + - - +
641A LEU 2.5 30.6 + - - -
642A PRO* 3.6 6.3 - - - +
643A MET* 3.4 61.5 - - + -
644A PRO* 3.9 1.6 - - + -
647A CYS* 3.7 7.9 - - - -
648A PRO 3.0 10.6 + - - +
649A PRO 3.7 5.8 - - - +
651A LEU* 1.3 75.3 - - - +
653A SER* 1.3 64.7 + - - +
655A MET* 3.0 21.7 + - - +
656A THR* 2.9 45.7 + - + +
659A TRP* 4.1 9.0 - + - -
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Residues in contact with SER 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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649A PRO 2.7 21.7 + - - -
650A THR* 3.5 10.5 - - - -
652A TYR* 1.3 75.3 - - - +
654A LEU* 1.3 60.0 - - - +
656A THR* 2.7 25.1 + - - -
657A LYS* 3.1 32.7 + - - +
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Residues in contact with LEU 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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612A MET* 4.5 4.0 - - + -
650A THR 3.1 12.5 + - - +
651A LEU* 3.1 13.2 + - + +
653A SER* 1.3 72.3 - - - +
655A MET* 1.3 68.5 + - - +
657A LYS* 3.2 26.6 + - + +
658A CYS* 3.3 14.1 + - - -
667A PRO* 4.9 7.6 - - + -
671A GLU* 5.9 0.2 - - + -
672A LEU* 3.4 33.7 - - + +
675A GLN* 4.0 35.4 - - + -
676A LEU* 3.6 33.9 - - + +
679A ILE* 4.3 6.5 - - + -
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Residues in contact with MET 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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609A GLY* 4.1 10.5 - - - +
612A MET* 3.7 46.6 - - + +
613A TRP* 3.8 26.7 - - - -
616A LEU* 3.9 21.5 - - + -
644A PRO* 4.4 1.8 - - + -
647A CYS* 3.9 15.9 - - - -
651A LEU* 3.0 19.7 + - + +
652A TYR* 3.0 26.1 + - + +
654A LEU* 1.3 76.5 - - - +
656A THR* 1.3 59.2 + - - +
658A CYS* 2.9 26.1 + - - +
659A TRP* 3.3 26.8 + - + -
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Residues in contact with THR 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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640A ARG* 5.4 6.9 + - + -
652A TYR* 2.9 47.9 + - + +
653A SER* 2.7 23.9 + - - -
655A MET* 1.3 75.8 - - - +
657A LYS* 1.3 64.0 + - - +
659A TRP* 3.0 33.4 + - + +
660A ALA* 3.5 1.7 + - - -
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Residues in contact with LYS 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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653A SER* 3.1 29.6 + - - +
654A LEU* 3.2 21.6 + - + +
656A THR* 1.3 78.4 - - - +
658A CYS* 1.3 60.9 + - - +
659A TRP 3.1 0.6 + - - -
660A ALA* 3.3 13.2 + - - +
665A ARG 4.4 1.9 - - - +
666A ARG* 3.7 7.3 - - - -
667A PRO* 3.3 28.9 - - + +
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Residues in contact with CYS 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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605A VAL* 3.5 38.1 - - - +
606A TRP* 3.3 20.4 - - - -
609A GLY* 3.8 10.8 - - - -
612A MET* 4.0 13.2 - - - -
654A LEU 3.3 17.4 + - - -
655A MET 2.9 11.0 + - - +
657A LYS* 1.3 75.8 - - - +
659A TRP* 1.3 58.2 + - + +
660A ALA 3.4 1.6 - - - -
666A ARG* 3.3 15.4 + - - -
667A PRO* 4.3 2.2 - - - -
672A LEU* 3.5 28.7 - - - -
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Residues in contact with TRP 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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606A TRP* 3.2 53.4 + + + -
609A GLY 3.4 23.1 - - - -
610A VAL* 3.4 13.2 - - + +
613A TRP* 4.1 11.7 - + + -
640A ARG* 2.9 53.3 + - + +
641A LEU* 3.7 51.1 - - + -
652A TYR* 4.1 7.6 - + - -
655A MET* 3.4 32.5 - - + -
656A THR* 3.0 20.0 + - + +
658A CYS* 1.3 84.2 - - + +
660A ALA* 1.3 64.7 + - - +
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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