Contacts of the helix formed by residues 713 - 725 (chain 4) 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 713 (chain 4).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7114 LYS* 3.0 41.3 - - - +
7124 VAL* 1.3 81.0 - - - +
7144 GLU* 1.3 58.6 + - - +
7154 LYS* 3.8 13.2 - - + +
7164 ASN* 2.9 35.1 + - + +
7174 ASP* 3.1 17.7 + - - +
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Residues in contact with GLU 714 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7124 VAL* 3.6 6.7 + - - +
7134 ASP* 1.3 70.4 - - - +
7154 LYS* 1.4 63.8 + - + +
7164 ASN 3.0 5.6 - - - -
7174 ASP* 3.9 2.3 - - - +
7184 ARG* 2.9 46.0 + - - +
6657 ILE* 3.1 51.3 - - - +
6667 ARG* 5.9 0.3 + - - -
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Residues in contact with LYS 715 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5314 TYR* 4.5 2.6 + - - -
7134 ASP* 3.8 11.2 - - + +
7144 GLU* 1.4 82.7 + - + +
7164 ASN* 1.3 56.5 + - - +
7184 ARG* 3.8 25.6 - - - +
7194 GLU* 4.1 16.6 - - - +
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Residues in contact with ASN 716 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5314 TYR* 3.1 29.3 + - - -
5324 GLU* 3.4 12.3 + - - +
7094 LEU 5.7 2.4 + - - -
7104 ASP* 5.5 2.8 + - - +
7114 LYS* 4.8 16.0 - - - +
7124 VAL 5.1 0.6 - - - +
7134 ASP* 2.9 37.2 + - + +
7154 LYS* 1.3 75.5 - - - +
7174 ASP* 1.3 72.2 + - - +
7184 ARG 3.3 0.9 - - - -
7194 GLU* 3.2 6.2 + - - +
7204 LEU* 2.8 31.8 + - - +
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Residues in contact with ASP 717 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7104 ASP* 4.6 2.6 - - - +
7124 VAL* 4.0 12.2 - - - +
7134 ASP 3.1 13.4 + - - +
7144 GLU* 4.4 2.2 - - - +
7164 ASN* 1.3 86.5 + - - +
7184 ARG* 1.3 60.7 + - - +
7204 LEU* 3.8 19.0 - - + +
7214 ALA* 2.9 25.1 + - - +
6617 VAL* 4.9 0.6 - - - +
6647 TYR* 5.3 8.2 - - + -
6657 ILE* 5.3 11.1 - - + +
6687 ARG* 3.2 41.5 + - + +
6727 LYS* 3.7 11.7 + - - -
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Residues in contact with ARG 718 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7144 GLU* 2.9 53.8 + - - +
7154 LYS* 3.8 21.3 - - - +
7174 ASP* 1.3 75.9 - - - +
7194 GLU* 1.3 64.3 + - - +
7204 LEU 3.1 0.4 - - - -
7214 ALA* 3.8 5.2 - - - -
7224 LYS* 2.8 51.5 + - + +
6587 ASP* 4.9 4.7 - - - -
6617 VAL* 3.5 23.8 - - + -
6627 GLN* 6.1 2.7 - - - -
6657 ILE* 4.3 8.8 - - + +
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Residues in contact with GLU 719 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5314 TYR* 3.1 42.5 - - + +
7154 LYS* 4.1 17.1 - - - +
7164 ASN 3.2 9.0 + - - +
7184 ARG* 1.3 83.7 + - - +
7204 LEU* 1.3 59.0 + - - +
7224 LYS* 3.9 13.3 + - - +
7234 HIS* 3.5 12.6 + - - +
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Residues in contact with LEU 720 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5314 TYR* 3.5 35.4 - - + +
7164 ASN* 2.8 19.1 + - - +
7174 ASP* 3.8 21.5 - - + +
7194 GLU* 1.3 77.3 - - - +
7214 ALA* 1.3 61.6 - - - +
7224 LYS 3.3 0.2 - - - -
7234 HIS* 3.1 4.5 - - - +
7244 LEU* 2.9 55.2 + - + +
6647 TYR* 5.5 5.6 - - + -
6687 ARG* 4.9 14.1 - - - +
6867 PRO* 5.4 4.5 - - + -
6897 LEU* 5.9 0.9 - - + -
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Residues in contact with ALA 721 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7174 ASP 2.9 20.4 + - - +
7184 ARG 3.3 6.0 + - - +
7204 LEU* 1.3 80.8 - - - +
7224 LYS* 1.3 49.3 - - - +
7234 HIS 3.0 0.2 - - - -
7244 LEU* 2.7 8.8 + - - +
7254 THR* 2.2 41.6 + - - -
6617 VAL* 3.7 29.8 - - + -
6647 TYR* 5.5 1.1 - - + -
6897 LEU* 4.5 17.3 - - + -
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Residues in contact with LYS 722 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7184 ARG* 2.8 46.5 + - + +
7194 GLU* 4.0 17.3 - - - +
7204 LEU 3.3 0.2 - - - -
7214 ALA* 1.3 75.7 - - - +
7234 HIS* 1.3 59.1 + - - +
7254 THR* 3.3 32.1 - - + +
7264 ASN* 4.0 12.0 + - - +
6547 GLU* 5.4 4.1 + - - -
6577 ASN* 5.9 1.3 - - - +
6587 ASP* 3.8 28.6 + - - +
6617 VAL* 4.0 10.8 - - - -
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Residues in contact with HIS 723 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5284 PRO 3.8 15.8 + - - -
5294 SER* 3.0 26.3 + - - -
5304 ILE 3.6 13.2 - - - -
5314 TYR* 3.8 26.0 - - + +
7194 GLU 3.5 10.4 + - - +
7204 LEU 3.1 14.5 + - - +
7214 ALA 3.0 0.2 - - - -
7224 LYS* 1.3 76.2 - - - +
7244 LEU* 1.3 76.3 - - + +
7254 THR 3.1 4.6 + - - -
7264 ASN* 3.6 24.9 + - - +
7274 LEU* 5.3 2.9 - - - +
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Residues in contact with LEU 724 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5294 SER 4.6 6.5 - - - +
5314 TYR* 5.6 1.1 - - + +
7204 LEU* 2.9 41.4 + - + +
7214 ALA* 2.7 10.5 + - - +
7234 HIS* 1.3 92.3 - - + +
7254 THR* 1.3 58.8 + - - +
7264 ASN 2.8 19.8 - - - +
7274 LEU* 4.8 9.0 - - + +
7284 TYR 5.2 0.2 + - - -
6867 PRO* 4.3 22.4 - - + +
6897 LEU* 5.3 11.4 - - + -
6937 ILE* 4.8 14.4 - - + +
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Residues in contact with THR 725 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7214 ALA 2.2 29.3 + - - -
7224 LYS* 3.3 36.9 - - + +
7234 HIS 3.1 0.2 - - - -
7244 LEU* 1.3 71.4 - - - +
7264 ASN* 1.3 56.9 + - - +
7284 TYR* 2.7 39.6 - - + +
6577 ASN* 3.2 38.7 + - - +
6617 VAL* 4.1 5.4 - - - +
6937 ILE* 6.1 1.8 - - - -
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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