Contacts of the helix formed by residues 642 - 657 (chain A) in PDB entry 3UGM
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 642 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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605A ASN* 6.1 0.2 - - - -
606A ILE 6.0 1.1 - - - -
607A GLY* 6.5 0.2 - - - -
611A ALA* 3.9 22.4 - - - -
636A ILE 3.5 17.8 + - - +
637A ALA* 4.5 3.8 - - - -
639A ASN 3.7 1.2 + - - -
640A GLY 3.4 4.9 + - - -
641A GLY* 1.3 70.1 - - - +
643A LYS* 1.3 60.5 + - - -
645A ALA* 4.1 1.3 - - - +
646A LEU* 2.9 35.3 + - - +
10B C 5.2 3.6 - - - -
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Residues in contact with LYS 643 (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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610A GLN* 3.5 43.9 + - + +
611A ALA* 4.5 0.2 - - - +
614A THR* 3.1 26.2 - - - +
641A GLY 3.4 1.4 + - - -
642A GLY* 1.3 70.1 - - - -
644A GLN* 1.3 68.6 + - - +
645A ALA 2.6 15.0 + - - -
646A LEU* 2.8 13.2 + - - -
647A GLU* 3.0 38.1 + - - +
10B C 3.6 19.7 + - - +
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Residues in contact with GLN 644 (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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641A GLY 4.2 1.8 + - - +
643A LYS* 1.3 89.3 - - + +
645A ALA* 1.3 55.9 + - - +
647A GLU* 3.8 17.5 - - - +
648A THR* 3.4 21.1 + - - -
651A ARG* 5.9 0.2 + - - -
677A LYS* 3.4 45.9 - - + +
10B C 4.2 26.1 + - - +
11B C 3.5 30.0 + - - +
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Residues in contact with ALA 645 (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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636A ILE* 4.3 4.3 - - + -
641A GLY* 3.9 28.2 + - - +
642A GLY 4.3 0.7 - - - +
643A LYS 2.6 5.5 + - - -
644A GLN* 1.3 73.8 - - - +
646A LEU* 1.3 62.9 + - - +
647A GLU 3.2 1.1 - - - -
648A THR* 3.8 0.8 + - - -
649A VAL* 3.3 26.2 + - - +
671A ALA* 3.8 25.9 - - + +
676A GLY* 4.4 3.8 - - - -
677A LYS* 4.2 19.3 - - - +
680A LEU* 4.1 2.8 - - - +
11B C 5.8 0.2 - - - +
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Residues in contact with LEU 646 (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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611A ALA 4.1 6.3 - - - +
614A THR* 3.5 43.7 - - + +
615A VAL* 4.1 10.5 - - + +
618A LEU* 4.1 11.5 - - + +
622A LEU* 4.6 15.9 - - + +
633A VAL* 3.7 31.6 - - + +
636A ILE* 4.2 20.8 - - + +
637A ALA* 4.9 6.5 - - - +
642A GLY 2.9 25.0 + - - +
643A LYS 2.8 6.8 + - - +
645A ALA* 1.3 74.7 - - - +
647A GLU* 1.3 63.9 + - - +
649A VAL* 3.3 18.4 - - + +
650A GLN* 3.4 4.9 + - - +
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Residues in contact with GLU 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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614A THR* 3.7 15.3 - - + +
617A ARG* 3.3 28.1 + - - +
618A LEU* 4.0 9.9 - - + -
643A LYS* 3.0 37.9 + - - +
644A GLN* 3.8 19.9 - - - +
646A LEU* 1.3 72.4 - - - +
648A THR* 1.3 55.5 + - - +
649A VAL 2.7 15.0 + - - -
650A GLN* 2.8 17.0 + - - +
651A ARG* 3.0 13.9 + - - +
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Residues in contact with THR 648 (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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644A GLN* 3.4 12.4 + - - -
645A ALA 3.8 0.6 + - - -
647A GLU* 1.3 75.9 - - - +
649A VAL* 1.3 52.8 + - - +
651A ARG* 2.9 33.0 + - - +
652A LEU* 2.6 47.4 + - + +
677A LYS* 3.5 23.7 - - - +
680A LEU* 3.3 40.5 - - + +
681A GLU* 4.7 2.3 - - + +
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Residues in contact with VAL 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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622A LEU* 3.8 18.6 - - + -
628A LEU* 4.4 9.9 - - + -
636A ILE* 4.7 9.2 - - + -
645A ALA 3.3 15.8 + - - +
646A LEU* 3.3 13.5 - - + +
647A GLU 2.7 5.1 + - - -
648A THR* 1.3 70.2 - - - +
650A GLN* 1.3 69.2 + - - +
652A LEU 3.0 0.6 + - - -
653A LEU* 2.6 51.7 + - + +
667A VAL* 4.2 14.6 - - + -
671A ALA* 3.6 24.2 - - + -
680A LEU* 4.1 7.6 - - + -
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Residues in contact with GLN 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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617A ARG* 5.4 4.0 + - - -
618A LEU* 4.4 22.6 - - + +
621A VAL* 4.1 17.4 - - + +
622A LEU* 4.6 5.8 - - + +
626A HIS* 4.0 24.1 + - + +
646A LEU 3.4 3.9 + - - +
647A GLU* 2.8 10.1 + - - +
649A VAL* 1.3 78.9 - - - +
651A ARG* 1.3 77.2 + - + +
653A LEU* 3.6 11.2 - - - -
654A PRO* 3.1 18.4 - - - +
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Residues in contact with ARG 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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647A GLU 3.0 10.4 + - - +
648A THR* 2.9 29.1 + - - +
650A GLN* 1.3 92.4 - - + +
652A LEU* 1.3 92.4 + - + +
654A PRO* 4.0 5.4 - - - +
655A VAL* 4.0 12.5 - - - +
677A LYS* 4.3 20.2 - - - +
681A GLU* 4.8 13.9 - - - +
684A GLN* 5.2 4.0 + - - -
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Residues in contact with LEU 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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648A THR* 2.6 32.1 + - + +
649A VAL* 3.5 0.4 - - - -
651A ARG* 1.3 118.4 - - + +
653A LEU* 1.3 58.0 + - - +
654A PRO* 3.6 1.3 - - - -
655A VAL* 4.0 28.0 - - + -
656A LEU* 3.1 45.8 + - + +
680A LEU* 5.5 3.4 - - + +
681A GLU* 4.9 12.6 - - - +
684A GLN* 5.0 17.3 - - + +
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Residues in contact with LEU 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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622A LEU* 4.0 4.7 - - + -
626A HIS* 4.0 23.8 - - + +
628A LEU* 3.8 32.8 - - + -
649A VAL* 2.6 49.8 + - + +
650A GLN* 3.6 8.1 - - - -
652A LEU* 1.3 71.6 - - - +
654A PRO* 1.4 79.8 - - + +
656A LEU* 4.1 2.8 - - - +
657A CYS* 3.3 26.0 + - - -
664A PRO* 5.7 6.5 - - + -
667A VAL* 4.2 28.7 - - + -
680A LEU* 6.5 0.2 - - - -
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Residues in contact with PRO 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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626A HIS* 3.7 26.5 - - + +
650A GLN 3.1 21.3 - - - +
651A ARG 4.0 3.6 - - - +
652A LEU 3.6 0.7 - - - -
653A LEU* 1.4 98.9 - - + +
655A VAL* 1.3 70.8 + - + +
657A CYS* 3.1 14.5 + - + +
658A GLN* 3.8 7.5 + - - +
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Residues in contact with VAL 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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651A ARG 4.0 15.7 - - - +
652A LEU* 4.0 26.7 - - + +
654A PRO* 1.3 80.2 - - + +
656A LEU* 1.3 55.9 + - + +
658A GLN* 2.6 63.7 + - - +
660A HIS* 5.5 3.5 - - + -
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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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652A LEU* 3.1 30.9 + - + +
653A LEU* 4.1 4.9 - - - +
654A PRO 3.4 0.2 + - - -
655A VAL* 1.3 80.2 - - + +
657A CYS* 1.3 60.8 + - - +
658A GLN 3.3 2.6 + - - -
660A HIS* 2.7 45.4 + - + +
661A GLY 3.7 1.7 + - - -
662A LEU* 3.9 29.2 - - + -
667A VAL* 4.2 13.9 - - + -
670A ILE* 5.8 0.2 - - + -
680A LEU* 4.3 24.7 - - + +
683A VAL* 4.1 12.6 - - + -
684A GLN* 4.0 33.4 - - + -
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Residues in contact with CYS 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 LEU* 3.3 19.5 - - - +
654A PRO* 3.1 9.3 + - + +
655A VAL 2.8 4.9 + - - -
656A LEU* 1.3 77.0 - - - +
658A GLN* 1.3 62.2 + - - +
661A GLY* 3.5 31.6 + - - +
662A LEU* 4.1 15.0 - - - -
664A PRO* 5.0 12.3 - - - -
667A VAL* 4.7 7.6 - - - -
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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