Contacts of the helix formed by residues 710 - 728 (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 710 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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675A GLY 4.5 4.0 + - - -
679A ALA* 4.1 16.8 - - - -
704A ILE 4.0 16.1 - - - +
705A ALA* 4.7 1.1 - - - -
707A ASN 3.0 10.5 + - - -
709A GLY* 1.3 72.4 - - - +
711A LYS* 1.3 55.7 + - - +
713A ALA* 2.6 32.1 + - - +
714A LEU* 3.3 15.3 + - - +
12B T 4.4 3.6 + - - -
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Residues in contact with LYS 711 (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* 3.8 22.4 - - + +
679A ALA* 4.1 9.9 - - - +
682A THR* 3.2 36.1 - - + +
685A ARG* 3.6 17.5 - - - +
709A GLY 3.8 0.2 - - - -
710A GLY* 1.3 71.1 - - - +
712A GLN* 1.3 90.2 + - - +
713A ALA 2.7 6.8 + - - -
714A LEU* 3.3 9.7 + - - +
715A GLU* 3.1 40.6 + - - +
719A ARG* 5.4 1.4 - - - +
12B T 3.6 11.0 + - - +
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Residues in contact with GLN 712 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709A GLY 3.6 6.2 + - - +
710A GLY 2.8 3.8 + - - -
711A LYS* 1.3 105.4 - - - +
713A ALA* 1.3 56.7 + - - +
715A GLU* 5.2 0.6 - - - +
716A THR* 3.2 11.2 + - - -
745A LYS* 2.8 49.4 - - + +
12B T 2.8 57.3 + - - +
13B A 3.3 20.9 - - - +
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Residues in contact with ALA 713 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704A ILE* 3.9 19.1 - - + +
709A GLY 3.6 4.9 + - - +
710A GLY* 2.6 16.3 + - - +
712A GLN* 1.3 74.1 - - - +
714A LEU* 1.3 67.7 + - - +
715A GLU 3.2 1.6 - - - -
716A THR* 2.8 4.1 + - - -
717A VAL* 2.7 27.4 + - - +
739A ALA* 4.1 6.7 - - + +
744A GLY* 3.9 26.5 - - - +
745A LYS 4.0 4.9 - - - +
748A LEU* 5.0 3.1 - - + -
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Residues in contact with LEU 714 (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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679A ALA 4.5 2.5 - - - +
682A THR* 3.6 43.7 - - + +
683A VAL* 3.7 24.2 - - + +
686A LEU* 4.5 7.4 - - + -
690A LEU* 4.8 10.5 - - + -
701A VAL* 4.7 11.7 - - + -
704A ILE* 3.0 39.3 - - + -
705A ALA* 4.7 7.6 - - + +
710A GLY 3.3 9.8 + - - +
711A LYS 3.3 1.2 + - - +
713A ALA* 1.3 77.6 - - - +
715A GLU* 1.3 64.8 + - - +
717A VAL* 2.8 23.0 + - + +
718A GLN* 2.9 15.6 + - - +
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Residues in contact with GLU 715 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682A THR* 4.7 0.8 - - - +
685A ARG* 5.3 2.7 - - - +
686A LEU* 4.1 16.1 - - + +
711A LYS* 3.1 40.3 + - + +
712A GLN 5.2 0.7 - - - +
713A ALA 3.2 0.2 - - - -
714A LEU* 1.3 78.0 - - - +
716A THR* 1.3 59.7 + - - +
718A GLN* 3.1 15.8 + - - +
719A ARG* 3.1 37.6 + - - +
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Residues in contact with THR 716 (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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712A GLN* 3.2 16.7 + - - -
713A ALA 2.8 8.9 + - - -
715A GLU* 1.3 73.1 - - - +
717A VAL* 1.3 61.2 + - - +
719A ARG* 4.1 12.5 + - - +
720A LEU* 3.4 34.2 + - + +
745A LYS* 3.3 50.0 + - + +
748A LEU* 3.8 17.2 - - + +
749A GLU* 4.7 4.3 + - + +
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Residues in contact with VAL 717 (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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690A LEU* 4.3 10.8 - - + -
704A ILE* 4.8 12.3 - - + -
713A ALA 2.7 17.1 + - - +
714A LEU* 2.8 28.7 - - + +
716A THR* 1.3 71.7 - - - +
718A GLN* 1.3 83.2 + - - +
719A ARG 3.2 1.6 - - - -
720A LEU* 4.3 2.5 - - - +
721A LEU* 2.8 33.5 + - + +
735A VAL* 3.8 13.2 - - + -
736A VAL* 6.2 0.2 - - + -
739A ALA* 3.7 18.8 - - + -
748A LEU* 3.6 32.1 - - + -
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Residues in contact with GLN 718 (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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686A LEU* 3.2 32.1 - - + +
689A VAL* 4.1 17.3 + - + -
690A LEU* 3.1 40.3 - - - +
694A HIS* 3.1 27.2 + - - -
714A LEU 2.9 18.6 + - - +
715A GLU 3.3 10.8 - - - +
717A VAL* 1.3 80.0 - - - +
719A ARG* 1.3 74.0 + - - +
722A PRO* 3.4 14.4 - - - +
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Residues in contact with ARG 719 (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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686A LEU* 5.7 1.6 - - - +
711A LYS* 5.4 1.2 - - - +
715A GLU* 3.1 45.7 + - - +
716A THR* 4.1 14.3 + - - +
717A VAL 3.2 0.4 - - - -
718A GLN* 1.3 93.4 - - - +
720A LEU* 1.3 69.2 + - + +
721A LEU 3.0 6.7 + - - -
722A PRO* 3.3 12.3 - - - +
723A VAL* 4.0 13.3 - - + +
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Residues in contact with LEU 720 (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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716A THR* 3.4 26.4 + - + +
717A VAL* 3.2 5.7 + - - -
719A ARG* 1.3 83.5 - - + +
721A LEU* 1.3 60.9 + - - +
723A VAL* 4.3 20.8 - - + +
724A LEU* 3.8 16.5 + - - +
735A VAL* 4.9 5.9 - - - +
748A LEU* 3.9 13.0 - - + +
749A GLU* 3.7 32.1 - - + +
752A GLN* 3.1 51.4 - - + +
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Residues in contact with LEU 721 (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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690A LEU* 5.4 0.4 - - + -
694A HIS* 3.3 46.9 - - + +
696A LEU* 3.9 20.2 - - + -
717A VAL* 2.8 22.6 + - + +
719A ARG 3.0 2.6 + - - -
720A LEU* 1.3 70.7 - - - +
722A PRO* 1.4 75.9 - - + +
723A VAL 3.0 0.7 - - - -
724A LEU* 2.8 15.6 + - - +
725A CYS* 3.4 33.3 + - - -
732A PRO* 4.8 9.6 - - + -
735A VAL* 4.3 29.6 - - + -
736A VAL* 5.9 0.2 - - + -
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Residues in contact with PRO 722 (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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694A HIS* 3.7 15.9 - - + -
718A GLN 3.4 10.1 - - - +
719A ARG 3.3 11.0 - - - +
721A LEU* 1.4 104.3 - - + +
723A VAL* 1.3 63.6 + - + +
724A LEU 3.4 0.2 + - - -
725A CYS* 4.8 2.7 - - - -
726A GLN* 3.1 47.6 + - + +
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Residues in contact with VAL 723 (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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719A ARG* 4.0 15.3 - - + +
720A LEU* 4.3 27.6 - - + +
721A LEU 2.9 0.8 + - - -
722A PRO* 1.3 78.8 - - + +
724A LEU* 1.3 58.6 + - + +
726A GLN* 4.4 0.6 - - - +
727A ALA* 3.2 31.5 + - + +
728A HIS* 3.9 17.4 + - + -
752A GLN* 4.8 9.9 - - + -
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Residues in contact with LEU 724 (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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720A LEU 3.8 12.1 + - - +
721A LEU 2.8 14.2 + - - +
723A VAL* 1.3 71.2 - - + +
725A CYS* 1.3 64.0 + - - +
726A GLN 2.9 2.3 + - - -
728A HIS* 2.7 41.9 + - + +
729A GLY 3.3 6.9 + - - -
730A LEU* 3.9 28.3 - - + -
735A VAL* 4.7 5.6 - - + -
751A VAL* 5.6 5.8 - - + -
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Residues in contact with CYS 725 (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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721A LEU* 3.4 39.5 - - - -
722A PRO* 4.7 2.0 - - - -
724A LEU* 1.3 76.8 - - - +
726A GLN* 1.3 64.6 + - - +
728A HIS 4.8 0.3 - - - -
729A GLY* 4.3 8.0 + - - -
730A LEU 2.7 31.2 + - - +
731A THR* 3.7 20.4 - - - +
732A PRO* 4.9 4.0 - - + -
735A VAL* 4.9 1.6 - - - -
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Residues in contact with GLN 726 (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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722A PRO* 3.1 35.7 + - + +
723A VAL* 4.4 0.6 - - - +
724A LEU 2.9 1.4 + - - -
725A CYS* 1.3 82.4 - - + +
727A ALA* 1.3 65.2 + - + +
728A HIS 5.1 0.5 - - - -
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Residues in contact with ALA 727 (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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723A VAL* 3.2 16.3 + - + +
726A GLN* 1.3 82.5 - - + +
728A HIS* 1.3 69.0 + - + +
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Residues in contact with HIS 728 (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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723A VAL* 3.9 25.6 + - + +
724A LEU* 2.7 22.5 + - + +
725A CYS 4.8 1.6 - - - -
726A GLN 3.6 0.6 - - - -
727A ALA* 1.3 81.8 - - + +
729A GLY* 1.3 59.5 + - - +
751A VAL* 5.7 0.4 - - - +
752A GLN* 4.6 15.7 - - - -
755A LEU* 3.6 37.5 - - + +
756A PRO* 3.2 37.1 - - + +
766A PRO* 6.0 3.9 - - - +
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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