Contacts of the helix formed by residues 702 - 707 (chain 6) 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 THR 702 (chain 6).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6112 LYS* 5.2 2.7 - - - -
6512 ASN* 4.3 4.7 + - - -
6542 GLY 3.9 14.6 + - - -
6496 GLN* 5.4 2.4 - - + +
6506 VAL* 3.9 13.9 - - + -
6966 ARG* 3.9 6.2 + - - +
7016 MET* 1.3 75.5 - - - +
7036 ALA* 1.3 58.6 + - - +
7046 PRO* 3.1 31.2 - - + +
7056 ILE* 3.2 24.8 + - + +
7066 MET* 2.8 25.2 + - - +
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Residues in contact with ALA 703 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5452 PRO* 3.7 24.5 - - + -
6552 GLY* 5.0 0.4 - - - -
6966 ARG* 3.3 33.3 - - - +
7026 THR* 1.3 68.6 + - - +
7046 PRO* 1.4 70.1 - - + +
7066 MET* 3.6 13.2 - - - -
7076 SER* 2.6 38.4 + - - -
7936 TYR* 4.9 5.8 - - + -
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Residues in contact with PRO 704 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5452 PRO* 4.1 11.7 - - + -
6112 LYS* 4.7 2.5 - - - +
6512 ASN* 3.7 28.3 - - + +
6542 GLY 5.0 0.9 - - - +
9012 ANP 3.0 45.5 + - - +
6506 VAL* 5.0 0.7 - - + -
6536 HIS* 2.7 25.1 + - - -
7026 THR* 3.1 27.4 - - + +
7036 ALA* 1.4 92.3 - - + +
7056 ILE* 1.3 52.8 + - + +
7086 ARG* 3.2 12.1 + - - +
7986 ARG* 4.0 3.5 + - - +
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Residues in contact with ILE 705 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6416 PHE* 5.3 0.9 - - + -
6496 GLN* 3.4 45.3 - - + +
6506 VAL* 3.4 32.5 - - + -
6536 HIS* 3.2 33.0 - - + -
7016 MET* 3.7 22.4 - - + -
7026 THR* 3.2 15.4 + - + +
7046 PRO* 1.3 75.4 - - - +
7066 MET* 1.3 61.5 + - - +
7086 ARG* 4.0 1.3 - - - -
7096 PHE* 3.1 47.7 - - + -
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Residues in contact with MET 706 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6956 LEU* 4.1 7.4 - - + +
6966 ARG* 3.4 62.4 - - + +
6996 LEU* 4.4 5.2 - - + -
7016 MET* 4.2 15.3 - - + +
7026 THR 2.8 17.2 + - - +
7036 ALA* 3.0 6.0 + - - -
7056 ILE* 1.3 77.4 - - - +
7076 SER* 1.3 62.4 + - - +
7086 ARG 2.9 5.4 + - - -
7096 PHE* 3.0 12.0 + - - +
7126 PHE* 2.9 40.1 - - + -
7916 SER 5.6 1.3 - - - +
7936 TYR* 3.1 37.4 + - + +
8386 VAL* 5.8 1.8 - - + -
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Residues in contact with SER 707 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5452 PRO* 5.1 4.7 - - - -
7036 ALA* 2.6 23.0 + - - -
7066 MET* 1.3 76.0 - - - +
7086 ARG* 1.3 53.2 + - - -
7106 ASP* 2.7 30.6 - - - +
7936 TYR* 3.3 29.6 - - - -
7966 THR* 2.5 30.9 + - - -
7986 ARG* 2.8 15.9 + - - -
7996 GLN* 3.3 2.9 + - - +
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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