Contacts of the helix formed by residues 514 - 517 (chain A) in PDB entry 6UPY
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 PRO 514 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452A LYS* 4.6 15.3 - - + +
453A MET* 4.1 11.9 - - + -
510A GLN* 5.0 2.7 - - - +
512A VAL 3.8 7.2 - - - +
513A SER* 1.3 84.1 - - - +
515A GLN* 1.3 61.7 + - - +
516A SER 3.3 3.1 + - - -
517A ASN* 3.4 4.5 + - - +
868A TYR* 6.0 0.4 - - - +
874A ASP* 4.4 9.0 - - - +
875A ALA* 3.2 35.7 - - + +
876A ALA* 4.0 16.8 - - + +
1062A GLU* 5.4 2.0 - - - +
1067A LEU* 3.8 31.2 - - + -
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Residues in contact with GLN 515 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A HIS* 3.2 38.0 + - - -
453A MET* 4.8 11.2 - - + +
513A SER* 2.5 33.7 + - - +
514A PRO* 1.3 77.8 - - - +
516A SER* 1.3 72.4 + - - +
517A ASN 3.1 1.3 + - - -
518A LYS* 5.4 0.2 + - - -
1067A LEU* 4.9 7.0 - - + +
1070A GLN 4.3 0.4 + - - -
1071A SER* 3.1 49.9 - - - +
1074A GLU* 3.7 17.0 - - - +
1075A PRO* 4.0 7.7 - - + +
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Residues in contact with SER 516 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A PRO 3.3 2.0 + - - -
515A GLN* 1.3 84.1 + - - +
517A ASN* 1.3 83.6 + - - +
518A LYS* 3.0 33.4 + - - +
626A ASN* 4.4 2.6 + - - +
1071A SER* 4.6 1.0 + - - -
1075A PRO* 5.6 3.5 - - - +
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Residues in contact with ASN 517 (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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512A VAL* 5.1 2.2 - - - -
513A SER 3.3 9.8 + - - -
514A PRO 3.4 4.6 + - - +
515A GLN 3.1 5.3 - - - -
516A SER* 1.3 88.5 + - - +
518A LYS* 1.3 57.9 + - - +
626A ASN* 3.1 18.3 + - - +
631A HIS* 3.5 19.8 - - - -
875A ALA* 3.3 27.6 - - + +
876A ALA 5.3 0.2 - - - -
878A ILE* 3.7 21.8 + - + +
880A LYS* 5.3 4.0 - - - +
955A PRO* 4.7 14.0 - - - +
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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
------------------------------------------------------------
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