Contacts of the helix formed by residues 799 - 804 (chain S) in PDB entry 4NYJ
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 VAL 799 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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795S LEU 3.6 16.4 - - - +
796S TYR* 3.8 10.3 - - - +
797S ARG 3.4 0.6 - - - -
798S ALA* 1.3 75.9 - - - +
800S GLN* 1.3 74.3 + - - +
801S PRO* 4.7 1.4 - - - +
803S GLU* 4.1 6.7 - - + -
804S LEU* 4.0 17.7 - - + +
820S ASN* 3.8 18.8 - - - +
821S LEU* 3.9 18.2 - - + -
824S MET* 4.8 4.3 - - - -
930S PHE* 3.8 32.8 - - + -
971S ILE* 5.2 2.0 - - + +
972S GLN* 6.0 0.7 - - - +
975S GLN* 3.0 23.7 + - - +
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Residues in contact with GLN 800 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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699S HIS 5.3 4.2 - - - +
702S TYR* 6.3 0.4 - - + -
797S ARG 4.0 8.5 + - - -
798S ALA* 3.4 20.9 + - - +
799S VAL* 1.3 84.9 + - - +
801S PRO* 1.3 75.9 - - + +
802S SER* 3.1 17.7 + - - +
803S GLU* 3.1 28.9 + - - +
804S LEU* 4.2 3.7 + - - +
820S ASN* 5.5 1.8 - - - +
972S GLN* 5.3 3.4 + - - +
975S GLN* 5.2 2.6 + - - +
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Residues in contact with PRO 801 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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629S THR* 4.3 26.5 - - + +
699S HIS 5.8 3.8 - - - +
700S HIS* 5.5 8.7 - - + +
702S TYR* 6.5 0.4 - - + -
799S VAL 4.7 1.3 - - - +
800S GLN* 1.3 92.9 - - + +
802S SER* 1.3 59.3 + - - +
803S GLU 3.1 0.9 - - - -
804S LEU* 3.1 22.3 + - + +
805S VAL* 3.1 20.2 + - - +
968S THR* 4.6 12.1 - - + -
972S GLN* 3.9 37.7 - - + +
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Residues in contact with SER 802 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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702S TYR* 3.4 52.3 + - - +
706S ARG* 4.3 14.5 + - - -
800S GLN* 3.8 15.2 - - - +
801S PRO* 1.3 78.6 - - - +
803S GLU* 1.3 63.1 + - - +
804S LEU 3.2 0.6 + - - -
805S VAL* 4.4 6.7 - - - +
808S VAL* 3.7 12.0 - - - +
817S ASN* 4.0 6.7 + - - +
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Residues in contact with GLU 803 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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798S ALA 3.9 0.5 - - - +
799S VAL* 4.5 1.6 - - + -
800S GLN* 3.2 35.8 + - - +
801S PRO 3.1 0.8 - - - -
802S SER* 1.3 82.3 - - - +
804S LEU* 1.3 70.0 + - + +
808S VAL* 3.3 7.7 - - - +
809S TRP* 3.8 7.1 - - - +
817S ASN 3.5 15.9 - - - +
818S SER* 2.8 33.9 + - - +
819S PRO* 4.6 2.9 - - - -
820S ASN* 3.0 54.3 + - - +
821S LEU* 3.2 12.3 + - + -
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Residues in contact with LEU 804 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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799S VAL* 4.0 17.9 - - + -
800S GLN 4.4 9.2 - - - +
801S PRO* 3.1 9.4 + - + +
802S SER 3.2 0.2 - - - -
803S GLU* 1.3 90.0 - - + +
805S VAL* 1.3 70.1 + - + +
807S SER* 3.1 15.6 + - - -
808S VAL* 4.4 0.7 - - - -
809S TRP* 3.1 16.9 - - + -
821S LEU* 3.9 24.7 - - + -
930S PHE* 4.3 7.6 - - + -
934S LEU* 4.5 10.3 - - + -
937S ILE* 4.0 26.6 - - + +
968S THR* 4.5 9.9 - - + -
971S ILE* 3.7 32.8 - - + -
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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