Contacts of the helix formed by residues 680 - 685 (chain A) in PDB entry 5UO5
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 680 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338A GLY 4.2 8.6 - - - +
418A SER* 3.0 13.1 + - - +
419A ARG* 3.1 49.0 + - + +
679A ALA* 1.3 70.4 - - - +
681A TRP* 1.3 52.2 + - - +
682A VAL* 3.1 26.0 + - - +
683A TRP* 2.9 10.4 + - - +
684A ILE* 2.7 34.5 + - - +
702A ASN* 3.8 25.7 + - - +
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Residues in contact with TRP 681 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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679A ALA 3.7 5.1 + - - -
680A ASP* 1.3 72.3 + - - +
682A VAL* 1.3 67.7 + - + +
684A ILE* 4.2 2.2 - - - -
685A VAL* 3.0 45.7 + - + +
695A VAL 3.2 10.8 + - - -
696A PHE* 3.0 51.8 + + - -
698A GLN 3.3 22.0 + - - -
700A MET* 3.8 17.2 - - + -
339B SER* 3.7 29.8 - - - +
681B TRP* 4.2 13.5 - + - -
682B VAL* 3.7 48.5 - - + -
685B VAL* 6.2 0.9 - - + -
802B H4B 3.4 18.2 - - - -
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Residues in contact with VAL 682 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A GLY* 3.5 26.5 - - - +
339A SER* 4.5 3.8 - - - -
680A ASP* 3.1 10.9 + - - +
681A TRP* 1.3 78.4 - - + +
683A TRP* 1.3 63.0 + - + +
685A VAL* 4.2 6.4 - - - +
802A H4B 3.1 46.0 + - - +
681B TRP* 3.7 42.4 - - + -
682B VAL* 4.2 17.0 - - + -
696B PHE* 5.1 0.5 - - - -
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Residues in contact with TRP 683 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A GLY 6.1 0.2 - - - -
341A MET* 4.3 14.9 - - + +
419A ARG* 3.6 70.5 - - + +
421A VAL* 5.8 0.7 - - - +
680A ASP* 2.9 13.1 + - - +
682A VAL* 1.3 85.8 - - + +
684A ILE* 1.3 63.5 + - - +
685A VAL 3.4 5.6 + - - +
686A PRO* 5.4 0.2 - - - +
711A TYR* 4.0 2.0 - - - -
801A HEM 3.4 68.4 - - + +
802A H4B 3.2 76.7 + + - -
803A M4R 3.9 12.8 - + + -
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Residues in contact with ILE 684 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418A SER 3.6 20.6 - - - +
419A ARG 3.9 3.8 - - - -
420A CYS 3.7 28.7 - - - +
421A VAL* 3.7 23.5 - - + +
594A MET* 5.5 2.6 - - - +
660A THR* 4.6 0.2 - - - +
663A PHE* 3.9 20.2 - - + -
680A ASP 2.7 32.1 + - - +
681A TRP 3.3 1.5 + - - +
683A TRP* 1.3 74.5 - - - +
685A VAL* 1.3 62.2 + - - +
686A PRO* 3.4 8.8 - - - +
695A VAL* 3.8 20.1 - - + +
700A MET* 3.8 30.5 - - + -
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Residues in contact with VAL 685 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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681A TRP* 3.0 59.6 + - + +
682A VAL 4.2 6.4 - - - +
683A TRP 3.6 9.6 - - - +
684A ILE* 1.3 76.1 - - + +
686A PRO* 1.3 82.4 - - + +
687A PRO* 4.5 0.9 - - - +
690A GLY* 3.9 20.0 - - - +
693A THR* 4.9 0.2 - - - +
695A VAL* 4.0 9.0 - - + +
696A PHE* 4.1 20.0 - - + -
802A H4B 5.1 3.1 + - - -
681B TRP* 6.1 2.0 - - + -
696B PHE* 5.4 3.8 - - - -
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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