Contacts of the helix formed by residues 702 - 711 (chain C) in PDB entry 3UEO
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 702 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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622A TYR* 3.3 12.9 + - - -
657A ALA* 4.1 14.6 - - - -
655C GLN* 5.2 0.7 - - - -
701C GLY* 1.3 76.8 - - - +
703C SER* 1.3 60.8 + - - -
704C LYS 3.3 3.5 + - - -
706C GLU* 3.1 27.9 + - - +
3F ASP* 6.4 2.0 - - - -
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Residues in contact with SER 703 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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655A GLN 6.1 0.5 - - - -
656A CYS 4.3 6.1 + - - -
657A ALA* 3.6 15.6 - - - +
702C GLY* 1.3 69.8 - - - -
704C LYS* 1.3 65.5 + - - +
706C GLU* 3.7 13.2 - - - +
707C ALA* 3.1 23.2 + - - +
6F TPO 3.9 36.3 + - - +
8F VAL* 3.6 7.4 - - - +
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Residues in contact with LYS 704 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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652C SER* 4.2 1.8 - - - -
653C PHE 2.6 35.3 + - - +
654C SER* 3.7 23.7 + - - +
661C LYS* 6.1 1.0 - - - +
677C GLU* 2.7 27.3 + - - -
679C PHE* 3.9 14.7 - - + +
695C LEU* 3.5 21.5 - - + +
702C GLY 3.3 0.6 - - - -
703C SER* 1.3 77.2 - - - +
705C TYR* 1.3 63.1 + - - +
707C ALA* 3.2 6.4 + - - +
708C ALA* 3.0 17.7 + - - +
3F ASP* 4.0 11.7 + - - +
5F ASP 5.0 0.2 - - - -
6F TPO 3.6 13.6 + - - +
7F ASP* 3.4 32.4 + - - +
8F VAL* 4.0 9.2 - - + -
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Residues in contact with TYR 705 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621A ASP 4.0 18.7 + - - -
622A TYR* 4.5 6.1 - + - -
654C SER* 5.0 0.4 + - - -
695C LEU* 3.5 10.3 - - - +
697C LEU* 3.9 16.1 - - + +
700C ARG* 3.7 25.2 - - + +
701C GLY* 3.1 39.1 + - - +
702C GLY 3.4 1.3 + - - +
704C LYS* 1.3 77.6 - - - +
706C GLU* 1.3 66.4 + - + +
708C ALA* 3.2 2.9 + - - +
709C LYS* 3.0 47.0 + - + +
715C ALA* 4.4 6.7 - - + -
738C ILE* 3.4 33.0 - - + -
739C GLU* 2.4 31.6 + - - -
712D ASN* 6.1 0.2 - - - -
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Residues in contact with GLU 706 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621A ASP* 5.2 5.3 - - + +
622A TYR* 3.3 25.1 + - + +
657A ALA* 4.2 6.0 - - - +
658A GLY* 3.5 33.3 + - - -
702C GLY 3.1 17.8 + - - +
703C SER* 3.9 8.6 - - - +
704C LYS 3.3 0.4 - - - -
705C TYR* 1.3 85.6 - - + +
707C ALA* 1.3 61.3 + - - +
709C LYS* 3.5 6.0 + - - +
710C LYS* 3.1 24.8 + - - +
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Residues in contact with ALA 707 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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679C PHE* 3.9 2.7 - - + -
703C SER 3.1 13.7 + - - +
704C LYS 3.5 8.3 - - - +
706C GLU* 1.3 75.0 - - - +
708C ALA* 1.3 56.5 + - - +
710C LYS* 4.4 5.4 - - - -
711C TRP* 2.7 66.1 + - + +
8F VAL* 3.7 24.7 - - + -
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Residues in contact with ALA 708 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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679C PHE* 3.6 22.3 - - + -
695C LEU* 4.1 3.4 - - + -
704C LYS 3.0 13.7 + - - +
705C TYR 3.2 8.7 + - - +
707C ALA* 1.3 76.3 - - - +
709C LYS* 1.3 61.0 - - + +
712C ASN* 2.9 19.4 + - - -
713C LEU* 3.0 30.0 + - - +
715C ALA* 3.7 22.4 - - + -
712D ASN* 3.8 0.8 + - - +
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Residues in contact with LYS 709 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621A ASP 5.2 3.2 + - - -
705C TYR* 3.0 42.8 + - + +
706C GLU* 4.0 6.1 - - - +
708C ALA* 1.3 75.8 - - + +
710C LYS* 1.3 63.0 + - - +
712C ASN* 3.4 9.5 + - - -
715C ALA* 6.0 0.2 - - + -
739C GLU* 3.1 36.2 + - - +
709D LYS* 3.8 31.6 - - - +
710D LYS* 3.5 21.3 + - - +
712D ASN* 4.1 21.5 - - + +
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Residues in contact with LYS 710 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577B GLU* 4.9 17.4 + - - +
578B ASN* 5.6 4.9 + - - +
623B GLN* 5.2 11.7 - - - +
681C ARG* 4.4 14.5 + - - +
706C GLU 3.1 19.1 + - - +
707C ALA* 3.8 4.9 - - - +
709C LYS* 1.3 77.8 - - - +
711C TRP* 1.3 76.0 + - + +
712C ASN 3.5 0.5 + - - -
709D LYS* 3.6 10.9 + - - +
739D GLU* 3.5 21.3 - - - +
10F GLU 6.0 1.5 + - - -
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Residues in contact with TRP 711 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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679C PHE* 3.3 40.6 - + - -
680C VAL 3.8 4.7 - - - -
681C ARG* 3.0 72.1 - - + +
707C ALA* 2.7 30.1 + - + +
708C ALA 4.1 1.6 - - - +
710C LYS* 1.3 90.1 - - + +
712C ASN* 1.3 67.4 + - - +
713C LEU* 3.3 16.7 + - + +
737D LEU* 3.3 16.1 - - - +
739D GLU* 4.1 10.5 - - - +
740D ASN* 4.7 2.6 + - - +
8F VAL* 3.7 24.0 - - + -
9F GLU 3.4 17.0 - - - -
10F GLU 3.6 18.4 + - - -
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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