Contacts of the helix formed by residues 688 - 703 (chain 2) in PDB entry 5U8T
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 ASP 688 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6852 ASP* 3.8 17.4 + - - +
6862 LEU 3.5 1.4 + - - -
6872 VAL* 1.3 78.5 - - - +
6892 GLU* 1.3 79.0 + - - +
6902 GLU* 4.1 7.6 + - - +
6912 ALA* 4.3 19.7 + - + +
6922 ASP* 3.0 28.7 + - - +
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Residues in contact with GLU 689 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6872 VAL* 5.3 3.0 - - - +
6882 ASP* 1.3 84.2 + - - +
6902 GLU* 1.3 66.1 + - + +
6912 ALA 3.4 0.2 + - - -
6922 ASP* 3.4 8.7 + - - +
6932 GLU* 2.9 31.4 + - - +
7786 LYS* 3.2 26.2 - - - +
7816 ARG 5.5 0.9 - - - -
7826 LYS* 3.4 31.8 - - + +
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Residues in contact with GLU 690 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6882 ASP* 4.1 5.5 + - - +
6892 GLU* 1.3 80.0 - - + +
6912 ALA* 1.3 59.8 + - - +
6932 GLU* 3.0 27.2 + - - +
6942 ARG* 2.9 55.4 + - - +
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Residues in contact with ALA 691 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6882 ASP* 4.3 22.4 + - + +
6892 GLU 3.4 0.8 - - - -
6902 GLU* 1.3 82.6 + - - +
6922 ASP* 1.3 64.8 + - - +
6942 ARG* 3.1 18.0 - - - +
6952 LEU* 2.9 28.1 + - - +
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Residues in contact with ASP 692 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6852 ASP* 5.3 4.2 - - - +
6872 VAL* 3.7 2.3 - - - +
6882 ASP* 3.0 20.7 + - - +
6892 GLU 3.4 6.7 + - - +
6902 GLU 3.2 0.6 - - - -
6912 ALA* 1.3 82.7 - - - +
6932 GLU* 1.3 60.0 + - - +
6942 ARG 3.2 0.2 - - - -
6952 LEU* 4.3 6.7 - - - +
6962 ALA* 2.9 35.7 + - + +
7776 TYR* 5.2 8.3 - - + -
7786 LYS* 6.0 1.8 - - + -
7816 ARG* 2.2 44.7 + - - +
7976 VAL* 5.4 5.4 - - - +
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Residues in contact with GLU 693 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6892 GLU* 2.9 37.8 - - - +
6902 GLU* 3.0 30.9 + - - +
6922 ASP* 1.3 73.8 - - - +
6942 ARG* 1.3 52.9 + - - +
6962 ALA* 4.9 0.9 - - - -
6972 THR* 2.3 45.6 + - + +
7786 LYS* 3.2 43.1 - - + +
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Residues in contact with ARG 694 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5062 TYR* 3.0 39.3 + - + +
6902 GLU* 2.9 39.8 + - - +
6912 ALA* 3.1 17.2 - - - +
6932 GLU* 1.3 74.0 - - - +
6952 LEU* 1.3 63.5 + - - +
6972 THR* 2.8 19.8 + - - -
6982 PHE* 3.0 12.6 + - - +
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Residues in contact with LEU 695 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5062 TYR* 3.5 22.7 - - + -
5072 GLY* 3.5 22.2 - - - +
5082 HIS* 5.6 5.4 - - + -
6912 ALA 2.9 18.8 + - - +
6922 ASP* 4.4 7.0 - - - +
6942 ARG* 1.3 74.4 - - - +
6962 ALA* 1.3 59.5 + - + +
6982 PHE* 3.1 7.6 - - - +
6992 VAL* 2.8 48.2 + - + +
9012 ANP 3.3 39.3 - - + +
7976 VAL* 3.8 21.3 - - + -
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Residues in contact with ALA 696 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6922 ASP* 2.9 21.8 + - + +
6932 GLU* 4.5 0.7 - - - +
6952 LEU* 1.3 76.9 - - + +
6972 THR* 1.3 60.4 + - - +
6982 PHE 3.1 0.7 - - - -
6992 VAL* 3.3 11.2 - - + +
7002 VAL* 2.9 34.8 + - - +
7746 VAL* 5.3 5.4 - - + -
7776 TYR* 4.1 18.4 - - + -
7786 LYS* 6.1 0.2 - - - +
7976 VAL* 6.1 2.0 - - + -
8006 LEU* 3.4 21.8 - - + -
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Residues in contact with THR 697 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6932 GLU* 2.3 38.0 + - + +
6942 ARG* 2.8 13.2 + - - -
6962 ALA* 1.3 72.7 - - - +
6982 PHE* 1.3 62.4 + - - +
7002 VAL* 3.5 1.8 + - - +
7012 ASP* 3.0 24.5 + - - +
7706 ARG* 5.5 0.3 + - - -
7746 VAL* 3.5 36.5 - - + +
7786 LYS* 4.8 1.1 - - - +
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Residues in contact with PHE 698 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5032 PRO 3.9 20.0 - - - -
5042 SER* 3.9 13.5 - - - -
5052 ILE 4.2 0.7 - - - -
5062 TYR* 3.3 52.9 - + + -
6942 ARG 3.0 10.4 + - - +
6952 LEU* 3.1 15.0 - - - +
6972 THR* 1.3 83.6 + - - +
6992 VAL* 1.3 58.7 + - + +
7012 ASP* 3.5 11.7 - - + +
7022 SER* 2.8 28.3 + - - -
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Residues in contact with VAL 699 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5042 SER 6.0 0.9 - - - +
5052 ILE 5.4 0.7 - - - +
6952 LEU* 2.8 44.0 + - + +
6962 ALA* 2.9 11.4 + - - +
6982 PHE* 1.3 77.9 - - + +
7002 VAL* 1.3 58.6 + - - +
7012 ASP 3.0 4.5 - - - -
7022 SER* 2.7 24.9 + - - +
7032 HIS* 2.9 42.7 + - + +
9012 ANP 4.9 13.9 - - + +
7976 VAL* 5.1 6.3 - - + +
8006 LEU* 3.6 23.1 - - + -
8016 GLU* 5.4 2.7 - - + +
8046 ILE* 5.2 1.6 - - + -
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Residues in contact with VAL 700 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6962 ALA 2.9 15.6 + - - +
6972 THR 4.2 2.0 - - - +
6992 VAL* 1.3 75.3 - - + +
7012 ASP* 1.3 57.8 + - - +
7022 SER 3.4 0.2 - - - -
7032 HIS* 4.2 2.6 - - + +
7042 VAL* 3.0 22.2 + - - +
7706 ARG* 3.1 42.4 + - + +
7736 LEU* 3.5 30.1 - - + -
7746 VAL* 4.6 13.2 - - + -
8006 LEU* 3.6 17.0 - - + -
8046 ILE* 4.7 14.8 - - + -
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Residues in contact with ASP 701 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6972 THR 3.0 18.7 + - - +
6982 PHE* 3.5 11.9 - - + +
6992 VAL 3.0 0.6 - - - -
7002 VAL* 1.3 78.4 - - - +
7022 SER* 1.3 63.7 + - - +
7042 VAL* 3.2 26.1 - - - +
7052 ARG* 4.9 2.6 - - - +
7706 ARG* 3.9 11.1 + - - +
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Residues in contact with SER 702 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5042 SER* 3.0 37.7 + - - -
6982 PHE* 2.8 21.2 + - - -
6992 VAL* 2.7 20.5 + - - -
7012 ASP* 1.3 68.0 - - - +
7032 HIS* 1.3 62.2 + - - -
7042 VAL 2.9 9.9 + - - -
7052 ARG* 3.2 13.6 - - - +
5596 THR* 3.0 22.7 + - - +
5656 LEU* 5.4 0.7 - - - +
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Residues in contact with HIS 703 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6992 VAL* 2.9 45.5 + - + +
7002 VAL 4.5 3.8 - - - +
7012 ASP 3.4 0.2 - - - -
7022 SER* 1.3 74.1 - - - +
7042 VAL* 1.3 55.9 + - - +
7052 ARG 2.9 23.9 - - - +
7062 SER* 5.0 1.7 - - - -
9012 ANP 5.9 8.5 - + - -
5556 VAL* 5.7 1.1 - - + -
5596 THR* 3.6 8.2 - - - +
5656 LEU* 3.5 37.9 - - + +
5666 ARG 4.6 2.0 - - - -
7646 ILE* 5.6 5.2 - - - +
8016 GLU* 3.9 26.0 - - + +
8046 ILE* 3.4 37.6 - - + +
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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