Contacts of the helix formed by residues 675 - 687 (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 675 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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673A ASN* 3.7 3.1 - - - +
674A GLY* 1.3 69.7 - - - +
676A GLY* 1.3 51.1 + - - -
677A LYS 3.8 0.9 - - - -
678A GLN* 3.5 3.9 - - - +
679A ALA* 2.8 38.1 + - - +
707A ASN 5.4 0.7 - - - -
709A GLY* 4.2 16.2 - - - +
710A GLY 4.5 3.5 + - - -
11B C 3.9 11.4 - - - +
12B T 3.0 30.5 + - - +
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Residues in contact with GLY 676 (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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645A ALA* 4.4 13.9 - - - -
670A ILE 4.2 14.3 - - - +
671A ALA* 4.8 0.9 - - - -
673A ASN* 3.9 11.2 - - - -
674A GLY 2.3 23.7 + - - -
675A GLY 1.3 61.0 - - - +
677A LYS* 1.3 68.3 + - - +
679A ALA* 3.0 13.7 + - - +
680A LEU* 3.2 18.8 + - - +
11B C 5.3 0.4 + - - -
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Residues in contact with LYS 677 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644A GLN* 3.4 54.5 - - + +
645A ALA* 4.2 7.4 - - - +
648A THR* 3.5 25.0 - - - +
651A ARG* 4.3 18.7 - - - +
674A GLY 4.7 0.4 + - - -
676A GLY* 1.3 72.7 - - - +
678A GLN* 1.3 74.0 + - - +
679A ALA 3.1 0.3 + - - -
680A LEU* 3.4 2.1 + - - +
681A GLU* 3.2 26.6 + - + +
11B C 3.4 26.7 + - - +
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Residues in contact with GLN 678 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675A GLY 3.5 3.5 + - - +
676A GLY 3.1 0.4 - - - -
677A LYS* 1.3 85.5 - - - +
679A ALA* 1.3 57.2 + - - +
681A GLU* 3.9 4.8 - - - +
682A THR* 2.8 36.1 + - - -
711A LYS* 4.1 22.4 - - + +
11B C 3.0 50.4 + - - +
12B T 3.4 17.7 + - - +
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Residues in contact with ALA 679 (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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670A ILE* 3.9 7.6 - - + +
675A GLY 2.8 21.3 + - - +
676A GLY 3.0 6.1 + - - +
678A GLN* 1.3 70.2 - - - +
680A LEU* 1.3 68.1 + - - +
682A THR* 2.8 15.1 + - - -
683A VAL* 2.8 16.4 + - - +
705A ALA* 3.7 27.1 - - - +
707A ASN 5.7 1.1 - - - +
710A GLY* 4.1 13.7 - - - -
711A LYS 4.1 9.2 - - - +
714A LEU* 4.5 2.0 - - - +
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Residues in contact with LEU 680 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645A ALA 4.1 3.1 - - - +
648A THR* 3.3 36.6 - - + +
649A VAL* 4.1 10.3 - - + +
652A LEU* 5.5 4.7 - - + -
656A LEU* 4.3 20.7 - - + +
667A VAL* 4.1 23.3 - - + -
670A ILE* 3.4 33.3 - - + +
671A ALA* 3.8 22.7 - - + +
676A GLY 3.2 14.7 + - - +
677A LYS 4.0 2.2 - - - +
679A ALA* 1.3 76.6 - - - +
681A GLU* 1.3 67.4 + - - +
683A VAL* 3.1 16.4 + - - +
684A GLN* 3.2 10.9 + - - +
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Residues in contact with GLU 681 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648A THR* 4.7 2.3 - - + +
651A ARG* 4.8 14.6 - - - +
652A LEU* 4.9 6.3 - - + -
677A LYS* 3.2 21.1 + - + +
678A GLN* 3.9 5.4 - - - +
679A ALA 3.2 1.0 - - - -
680A LEU* 1.3 75.8 - - - +
682A THR* 1.3 54.8 + - - +
683A VAL 2.6 13.3 + - - -
684A GLN* 2.5 46.3 + - - +
685A ARG* 5.0 4.7 - - - +
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Residues in contact with THR 682 (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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678A GLN* 2.8 22.0 + - - -
679A ALA 2.8 8.9 + - - -
681A GLU* 1.3 72.5 - - - +
683A VAL* 1.3 55.7 - - - +
685A ARG* 3.2 43.4 + - + +
686A LEU* 3.0 26.4 + - + -
711A LYS* 3.2 26.4 - - + +
714A LEU* 3.6 33.0 - - + +
715A GLU* 4.7 3.8 - - + +
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Residues in contact with VAL 683 (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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656A LEU* 4.1 15.7 - - + -
662A LEU* 4.1 13.7 - - + -
670A ILE* 5.0 5.4 - - + -
679A ALA 2.8 6.3 + - - +
680A LEU* 3.4 14.6 - - - +
681A GLU 2.6 5.3 + - - -
682A THR* 1.3 71.5 - - - +
684A GLN* 1.3 67.2 + - - +
685A ARG 2.9 1.3 - - - -
686A LEU 4.6 0.2 - - - +
687A LEU* 3.0 49.6 + - + +
701A VAL* 4.1 18.6 - - + -
705A ALA* 3.5 30.5 - - + -
714A LEU* 3.7 13.9 - - + -
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Residues in contact with GLN 684 (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* 5.2 3.3 + - - -
652A LEU* 5.0 19.0 - - + +
656A LEU* 4.0 22.7 - - + -
660A HIS* 4.1 18.4 + - + -
680A LEU 3.2 7.4 + - - +
681A GLU* 2.5 44.9 + - - +
683A VAL* 1.3 74.2 - - - +
685A ARG* 1.3 84.8 + - - +
688A PRO* 4.2 4.7 - - - +
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Residues in contact with ARG 685 (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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681A GLU* 3.0 8.7 + - - +
682A THR* 3.2 50.3 + - - +
683A VAL 2.9 1.0 - - - -
684A GLN* 1.3 99.3 - - - +
686A LEU* 1.3 83.9 + - + +
687A LEU 3.8 0.3 + - - -
688A PRO* 3.9 7.4 - - - +
689A VAL* 4.3 6.9 - - - +
711A LYS* 3.6 24.9 - - - +
715A GLU* 5.3 0.8 - - - +
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Residues in contact with LEU 686 (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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682A THR* 3.0 15.3 + - + +
683A VAL* 4.0 0.4 - - - -
685A ARG* 1.3 108.2 - - + +
687A LEU* 1.3 66.0 + - - +
688A PRO 3.3 1.8 - - - -
689A VAL* 3.9 19.5 - - + +
690A LEU* 2.9 32.3 + - + +
714A LEU* 4.5 6.5 - - + -
715A GLU* 4.1 20.4 - - + +
718A GLN* 3.2 43.5 - - + +
719A ARG* 5.7 0.9 - - - +
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Residues in contact with LEU 687 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660A HIS* 3.1 31.9 - - + +
662A LEU* 3.8 21.3 - - + -
683A VAL* 3.0 36.4 + - + +
686A LEU* 1.3 79.3 - - - +
688A PRO* 1.4 70.6 - - + +
690A LEU* 3.3 11.3 - - - +
691A CYS* 3.2 31.6 - - - -
698A GLN* 4.1 30.1 - - + +
701A VAL* 4.3 24.9 - - + -
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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