Contacts of the helix formed by residues 702 - 711 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622B TYR* 3.4 12.1 + - - -
657B ALA* 4.1 15.0 - - - +
654D SER* 5.8 1.8 - - - -
655D GLN* 5.1 0.7 - - - -
701D GLY* 1.3 76.6 - - - +
703D SER* 1.3 60.1 + - - -
704D LYS 3.3 3.3 + - - -
705D TYR 3.5 0.2 + - - -
706D GLU* 3.1 27.0 + - - +
1E PHE 5.8 2.2 - - - -
2E ILE* 6.0 5.6 - - - -
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Residues in contact with SER 703 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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655B GLN 6.1 0.2 - - - -
656B CYS 4.3 5.7 + - - -
657B ALA* 3.8 14.1 - - - +
702D GLY* 1.3 69.8 - - - -
704D LYS* 1.3 66.2 + - - +
706D GLU* 3.7 12.8 - - - +
707D ALA* 3.1 23.9 + - - +
6E TPO 3.6 38.6 + - - +
8E VAL* 3.5 6.8 - - - +
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Residues in contact with LYS 704 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652D SER* 4.2 5.1 - - - -
653D PHE 2.6 30.9 + - - +
654D SER* 3.7 17.4 + - - +
661D LYS* 6.1 0.4 - - - +
677D GLU* 2.7 26.4 + - - -
679D PHE* 3.9 14.7 - - + +
695D LEU* 3.5 20.7 - - + +
702D GLY 3.3 0.8 - - - -
703D SER* 1.3 80.6 - - - +
705D TYR* 1.3 63.7 + - - +
707D ALA* 3.3 3.9 + - - +
708D ALA* 3.1 17.7 + - - +
3E ASP* 3.6 17.2 + - - +
5E ASP 5.1 0.2 - - - -
6E TPO 3.6 13.4 + - - +
7E ASP* 3.4 33.5 + - - +
8E VAL* 3.8 10.8 - - + -
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Residues in contact with TYR 705 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621B ASP 4.1 13.8 + - - -
622B TYR* 4.6 5.6 - + - -
712C ASN* 6.3 0.2 - - - -
654D SER* 5.0 0.4 + - - -
695D LEU* 3.5 10.3 - - - +
697D LEU* 3.9 15.8 - - + +
700D ARG* 3.7 28.9 - - + +
701D GLY* 3.1 37.4 + - - +
702D GLY 3.5 2.4 + - - +
704D LYS* 1.3 79.3 - - - +
706D GLU* 1.3 66.1 + - + +
708D ALA* 3.3 3.2 + - - +
709D LYS* 3.1 47.3 + - + +
715D ALA* 4.4 7.2 - - + -
738D ILE* 3.4 32.1 - - + -
739D GLU* 2.5 32.2 + - - -
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Residues in contact with GLU 706 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621B ASP* 5.4 3.6 - - - +
622B TYR* 3.5 22.2 + - + +
657B ALA* 3.8 7.0 - - - +
658B GLY* 3.4 35.7 + - - -
702D GLY 3.1 16.5 + - - +
703D SER* 3.9 8.9 - - - +
704D LYS 3.3 0.8 - - - -
705D TYR* 1.3 82.1 - - + +
707D ALA* 1.3 64.8 + - - +
709D LYS* 3.6 6.0 + - - +
710D LYS* 3.1 25.3 + - - +
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Residues in contact with ALA 707 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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679D PHE* 3.9 5.8 - - + -
703D SER 3.1 17.5 + - - +
704D LYS 3.5 4.3 - - - +
706D GLU* 1.3 76.2 - - - +
708D ALA* 1.3 55.6 + - - +
710D LYS* 3.2 5.5 + - - -
711D TRP* 2.7 63.0 + - + +
8E VAL* 3.8 25.1 - - + -
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Residues in contact with ALA 708 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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712C ASN* 3.7 0.8 + - - +
679D PHE* 3.6 22.1 - - + -
695D LEU* 4.1 2.9 - - + -
704D LYS 3.1 12.9 + - - +
705D TYR 3.3 8.9 + - - +
707D ALA* 1.3 76.3 - - - +
709D LYS* 1.3 63.4 + - - +
711D TRP* 3.7 0.4 - - - -
712D ASN* 2.9 19.4 + - - -
713D LEU* 3.0 30.2 + - - +
715D ALA* 3.7 22.0 - - + -
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Residues in contact with LYS 709 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621B ASP 5.3 3.4 + - - -
709C LYS* 3.8 32.2 - - - +
710C LYS* 3.6 20.9 + - - +
712C ASN* 4.1 21.0 + - + +
705D TYR* 3.1 41.6 + - + +
706D GLU* 3.9 5.8 - - - +
707D ALA 3.3 0.2 - - - -
708D ALA* 1.3 76.6 - - + +
710D LYS* 1.3 64.0 + - - +
712D ASN* 3.3 9.9 + - - -
715D ALA* 5.9 0.2 - - + -
739D GLU* 3.1 35.2 + - - +
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Residues in contact with LYS 710 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577A GLU* 4.7 18.2 + - - +
578A ASN* 5.5 5.1 + - - +
623A GLN* 5.2 12.8 - - - +
709C LYS* 3.5 11.1 + - - +
739C GLU* 3.5 21.6 - - - +
681D ARG* 4.4 14.5 + - - +
706D GLU 3.1 18.7 + - - +
707D ALA* 3.7 5.6 - - - +
709D LYS* 1.3 76.8 - - - +
711D TRP* 1.3 74.4 + - + +
712D ASN 3.5 0.5 + - - -
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Residues in contact with TRP 711 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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737C LEU* 3.2 17.3 - - - +
739C GLU* 4.0 10.9 - - - +
740C ASN* 4.7 2.1 + - - -
679D PHE* 3.3 41.1 - + - -
680D VAL 3.8 4.0 - - - -
681D ARG* 3.0 72.7 - - + +
707D ALA* 2.7 31.0 + - + +
708D ALA 4.1 2.0 - - - +
710D LYS* 1.3 88.0 - - + +
712D ASN* 1.3 70.1 + - - +
713D LEU* 4.1 17.7 - - + -
8E VAL* 3.6 23.6 - - + -
9E GLU 3.1 26.7 - - - -
10E GLU 4.0 12.4 + - - -
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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