Contacts of the helix formed by residues 800 - 811 (chain S) in PDB entry 1NVU
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 GLN 800 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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699S HIS 5.5 2.6 - - - +
797S ARG 4.1 7.3 + - - -
798S ALA* 3.4 26.1 + - - +
799S VAL* 1.3 82.6 + - - +
801S PRO* 1.3 78.8 - - + +
802S SER* 3.2 14.6 - - - +
803S GLU* 2.8 33.9 + - + +
804S LEU* 3.9 3.4 - - - +
820S ASN* 4.9 4.3 - - - +
972S GLN* 5.5 1.6 + - - -
975S GLN* 5.7 0.6 + - - -
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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
----------------------------------------------------------
629S THR* 4.1 27.6 - - + +
699S HIS 6.1 0.9 - - - +
700S HIS* 5.7 7.4 - - + -
799S VAL 4.5 2.2 - - - +
800S GLN* 1.3 90.7 - - + +
802S SER* 1.3 56.6 + - - +
803S GLU 3.0 5.8 - - - -
804S LEU* 2.8 31.0 + - + +
805S VAL* 3.1 17.6 + - - +
968S THR* 4.5 11.7 - - + -
972S GLN* 3.6 35.4 - - + +
975S GLN* 6.0 0.2 - - - +
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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
----------------------------------------------------------
702S TYR* 3.6 45.6 - - - -
706S ARG* 4.6 10.1 + - - -
800S GLN* 4.1 8.8 - - - +
801S PRO* 1.3 80.1 - - - +
803S GLU* 1.3 68.4 + - - +
804S LEU 3.2 1.6 + - - -
805S VAL* 4.4 9.2 - - - +
808S VAL* 3.6 13.5 - - - +
817S ASN* 4.3 4.7 + - - +
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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
----------------------------------------------------------
798S ALA 3.6 0.2 - - - +
799S VAL* 4.2 7.6 - - + -
800S GLN* 2.8 36.6 + - + +
801S PRO 3.0 1.0 - - - -
802S SER* 1.3 84.9 - - - +
804S LEU* 1.3 64.1 + - + +
808S VAL* 3.2 8.7 - - - +
809S TRP* 3.9 6.1 - - - +
817S ASN 3.4 22.2 - - - +
818S SER* 2.8 30.8 + - - +
819S PRO* 4.4 2.7 - - + -
820S ASN* 3.0 38.0 + - - +
821S LEU* 2.9 27.7 + - + -
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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
----------------------------------------------------------
799S VAL* 4.2 10.1 - - + +
800S GLN 3.9 12.6 - - - +
801S PRO* 2.8 11.0 + - + +
803S GLU* 1.3 88.9 - - - +
805S VAL* 1.3 66.5 + - - +
807S SER 3.0 13.9 + - - -
808S VAL* 4.6 0.4 - - - -
809S TRP* 3.2 17.4 - - + -
821S LEU* 4.1 10.3 - - + -
930S PHE* 4.0 14.8 - - + -
934S LEU* 3.9 26.5 - - + -
937S ILE* 4.0 24.9 - - + +
968S THR* 4.3 12.1 - - + -
971S ILE* 3.6 33.7 - - + -
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Residues in contact with VAL 805 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629S THR* 3.6 41.3 - - + +
630S THR* 4.6 14.8 - - + +
632S ARG* 6.6 0.7 - - + -
633S SER* 6.1 4.3 - - - +
801S PRO 3.1 15.1 + - - +
802S SER* 4.4 6.9 + - - +
804S LEU* 1.3 78.5 - - - +
806S GLY* 1.3 67.2 + - - +
807S SER 3.3 0.3 + - - -
808S VAL* 3.6 18.4 - - - +
941S GLU* 4.4 8.5 - - - +
964S VAL* 4.4 18.8 - - + -
968S THR* 4.8 4.3 - - + -
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Residues in contact with GLY 806 (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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805S VAL* 1.3 77.3 - - - +
807S SER* 1.3 72.3 + - - +
808S VAL* 3.1 9.5 + - - +
811S LYS* 3.3 18.0 + - - -
941S GLU* 3.1 19.6 + - - -
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Residues in contact with SER 807 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804S LEU 3.0 12.8 + - - -
806S GLY* 1.3 78.2 - - - +
808S VAL* 1.3 62.1 + - - +
809S TRP* 3.2 16.0 - - - -
810S THR* 2.7 31.6 + - - -
811S LYS* 3.7 9.5 - - - +
937S ILE* 4.7 0.3 + - - +
938S LEU* 3.4 37.4 - - - +
941S GLU* 2.8 21.0 + - - +
942S GLU* 5.6 0.2 - - - +
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Residues in contact with VAL 808 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802S SER 3.6 12.6 - - - +
803S GLU* 3.2 33.4 - - - +
804S LEU 4.0 0.6 + - - -
805S VAL 3.6 14.8 - - - +
806S GLY* 4.0 7.9 - - - +
807S SER* 1.3 76.7 - - - +
809S TRP* 1.3 59.8 + - - +
810S THR 3.1 2.4 + - - -
811S LYS* 3.2 23.4 + - + +
813S ASP 4.7 0.5 - - - -
814S LYS* 3.6 14.7 + - - -
817S ASN* 4.0 28.2 + - + +
818S SER* 3.5 6.3 - - - +
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Residues in contact with TRP 809 (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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60R GLY* 2.9 27.3 + - - -
62R GLU* 5.9 0.2 - - - -
63R GLU* 4.6 14.9 - - + +
803S GLU 3.9 8.3 - - - -
804S LEU* 3.2 34.5 - - + -
807S SER* 3.1 14.7 + - - -
808S VAL* 1.3 76.0 - - - +
810S THR* 1.3 76.5 + - + +
814S LYS* 3.4 28.3 - - + +
818S SER* 3.3 21.5 + - - +
821S LEU* 3.4 26.5 - - + -
822S LEU* 5.0 5.4 - - + +
825S ILE* 5.4 0.9 - - + -
934S LEU* 3.3 52.8 - - + +
937S ILE* 4.1 15.5 - - + -
938S LEU* 4.2 7.4 - - + -
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Residues in contact with THR 810 (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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12R GLY* 4.8 4.6 - - - +
13R GLY* 4.6 24.8 + - - -
60R GLY* 4.4 11.0 - - - -
62R GLU* 4.9 5.4 - - - +
1003R PO4 5.1 2.0 - - - +
807S SER* 2.7 24.2 + - - +
809S TRP* 1.3 114.6 - - + +
811S LYS* 1.3 70.6 + - - +
814S LYS* 5.0 3.0 - - - +
938S LEU* 4.5 15.8 - - + +
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Residues in contact with LYS 811 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806S GLY 3.3 20.6 + - - -
807S SER* 3.7 12.8 - - - +
808S VAL* 3.2 17.6 + - + +
810S THR* 1.3 94.9 - - - +
812S GLU* 1.3 65.7 + - + +
813S ASP* 3.2 5.8 - - + +
814S LYS* 3.1 25.5 + - - +
817S ASN* 6.2 1.1 - - - +
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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