Contacts of the helix formed by residues 704 - 719 (chain A) in PDB entry 1CJY
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 ASN 704 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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619A GLU* 3.1 27.0 + - - +
620A CYS* 3.0 29.7 + - - +
640A PHE* 4.0 16.4 - - + -
700A ASN 3.5 13.0 + - - +
701A THR 3.2 4.7 + - - -
702A LEU 2.9 0.8 - - - -
703A ASN* 1.3 93.8 + - - +
705A ILE* 1.3 66.8 + - - +
706A ASP* 3.2 6.5 - - - -
707A VAL* 3.0 34.0 + - + +
708A ILE* 3.6 7.4 + - - +
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Residues in contact with ILE 705 (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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172A LEU* 6.2 1.3 - - + -
215A SER* 5.7 8.1 - - - -
217A ILE* 5.5 8.7 - - + -
701A THR 3.4 7.3 + - - +
702A LEU* 3.4 15.7 + - + +
704A ASN* 1.3 75.1 - - - +
706A ASP* 1.3 59.8 + - - +
708A ILE* 2.7 36.1 + - - +
709A LYS* 2.9 25.9 + - + +
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Residues in contact with ASP 706 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702A LEU 4.7 0.9 - - - +
703A ASN 4.1 8.1 - - - +
704A ASN* 3.5 7.8 + - - -
705A ILE* 1.3 84.3 + - - +
707A VAL* 1.3 68.3 + - - +
709A LYS* 3.8 18.3 - - - +
710A GLU* 2.9 30.1 + - - +
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Residues in contact with VAL 707 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620A CYS* 4.5 10.8 - - - -
622A VAL* 3.5 31.4 - - + -
638A ILE* 3.8 7.7 - - + +
704A ASN* 3.0 36.3 + - + +
705A ILE 3.0 0.2 + - - -
706A ASP* 1.3 86.0 - - - +
708A ILE* 1.3 58.8 + - + +
710A GLU* 3.6 6.4 - - + +
711A ALA* 3.1 24.1 + - - +
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Residues in contact with ILE 708 (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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212A LEU* 4.8 11.9 - - + -
217A ILE* 4.1 15.7 - - + -
570A LEU* 4.8 0.9 - - + -
572A ILE* 3.5 33.0 - - + -
638A ILE* 3.8 20.0 - - + -
640A PHE* 4.1 25.1 - - + -
701A THR* 5.0 5.4 - - + +
704A ASN 4.1 9.0 - - - +
705A ILE* 2.7 20.5 + - - +
707A VAL* 1.3 69.8 - - + +
709A LYS* 1.3 66.4 + - - +
710A GLU 3.0 0.9 - - - -
711A ALA* 2.9 2.9 + - - +
712A MET* 2.8 52.6 + - + +
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Residues in contact with LYS 709 (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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172A LEU* 3.6 51.6 - - + +
173A LEU* 4.5 16.6 + - + +
217A ILE* 5.4 1.1 - - + -
705A ILE* 2.9 28.3 + - + +
706A ASP* 3.8 13.8 - - - +
708A ILE* 1.3 77.0 - - - +
710A GLU* 1.3 62.9 + - - +
712A MET* 3.3 8.1 + - - +
713A VAL* 3.1 28.5 + - + +
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Residues in contact with GLU 710 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706A ASP 2.9 19.0 + - - +
707A VAL* 3.6 8.1 - - - +
709A LYS* 1.3 77.3 - - - +
711A ALA* 1.3 56.9 + - - +
713A VAL* 3.1 9.5 + - - +
714A GLU* 2.9 43.4 + - + +
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Residues in contact with ALA 711 (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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570A LEU* 3.9 15.2 - - + +
622A VAL* 5.5 5.6 - - + -
624A LYS* 6.0 2.7 - - + -
636A THR* 4.6 8.3 - - - +
638A ILE* 3.5 34.5 - - + -
707A VAL 3.1 4.7 + - - +
708A ILE 2.9 4.0 + - - +
710A GLU* 1.3 79.2 - - - +
712A MET* 1.3 51.8 + - - +
714A GLU* 3.8 13.0 + - - +
715A SER* 2.7 36.1 + - - -
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Residues in contact with MET 712 (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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169A MET* 3.9 40.4 - - + -
172A LEU* 3.7 29.4 - - + -
173A LEU* 4.0 11.4 - - + -
188A PRO* 5.3 1.3 - - + -
190A VAL* 4.6 3.1 - - + -
217A ILE* 3.9 9.6 - - + -
220A CYS* 4.5 9.9 - - + -
570A LEU* 3.6 19.5 - - + -
572A ILE* 4.9 2.2 - - + -
708A ILE* 2.8 37.4 + - + +
709A LYS* 3.5 8.1 - - - +
711A ALA* 1.3 74.5 - - - +
713A VAL* 1.3 54.8 + - - +
715A SER* 2.7 12.1 + - - -
716A ILE* 2.7 39.5 + - - +
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Residues in contact with VAL 713 (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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173A LEU* 4.0 15.0 - - + -
177A ASN* 3.9 35.0 - - + +
709A LYS* 3.1 15.9 + - + +
710A GLU* 3.3 9.9 - - - +
712A MET* 1.3 79.4 - - - +
714A GLU* 1.3 65.3 + - + +
716A ILE* 3.1 13.3 + - + +
717A GLU* 3.1 23.3 + - + +
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Residues in contact with GLU 714 (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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624A LYS* 3.3 39.2 + - + +
710A GLU* 2.9 32.3 + - + +
711A ALA* 3.9 10.6 + - - +
713A VAL* 1.3 81.0 - - + +
715A SER* 1.3 61.2 + - - +
717A GLU* 3.5 8.1 + - - +
718A TYR* 3.2 22.3 + - - +
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Residues in contact with SER 715 (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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188A PRO* 4.0 22.5 - - - +
569A ASP* 4.1 8.7 + - - +
570A LEU* 3.9 10.1 - - - +
636A THR* 3.8 20.8 - - - +
711A ALA 2.7 20.4 + - - -
712A MET* 2.7 20.9 + - - -
714A GLU* 1.3 69.8 - - - +
716A ILE* 1.3 61.3 + - - -
718A TYR* 3.2 9.5 + - - +
719A ARG* 3.1 21.0 + - - +
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Residues in contact with ILE 716 (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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169A MET* 4.6 2.7 - - - -
173A LEU* 3.5 32.5 - - + -
177A ASN 4.8 5.6 - - - +
178A SER* 5.3 0.9 - - - -
180A GLY* 4.0 24.9 - - - +
181A LEU* 3.6 39.5 - - + +
184A ALA* 5.1 2.5 - - + -
188A PRO* 4.4 14.6 - - + -
712A MET 2.7 22.1 + - - +
713A VAL* 3.1 10.3 + - + +
715A SER* 1.3 72.8 - - - +
717A GLU* 1.3 58.6 + - - +
718A TYR 3.0 0.2 - - - -
719A ARG* 2.9 33.0 + - + +
720A ARG* 3.5 2.8 + - - +
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Residues in contact with GLU 717 (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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713A VAL* 3.1 16.0 + - + +
714A GLU* 3.9 8.5 - - - +
715A SER 3.4 0.2 - - - -
716A ILE* 1.3 76.6 - - - +
718A TYR* 1.3 59.9 + - - +
720A ARG* 3.4 22.5 + - - +
721A GLN* 5.2 1.7 - - - +
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Residues in contact with TYR 718 (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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633A ASP* 4.5 23.4 - - - +
714A GLU 3.2 13.0 + - - +
715A SER* 3.2 12.8 + - - +
716A ILE 3.0 0.2 - - - -
717A GLU* 1.3 73.4 - - - +
719A ARG* 1.3 58.0 + - - +
720A ARG 2.9 9.9 + - - -
721A GLN* 3.4 20.5 + - - +
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Residues in contact with ARG 719 (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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184A ALA* 6.5 0.9 - - + -
185A ARG* 5.7 4.3 + - - +
186A ASP 4.1 19.8 + - - +
187A VAL 5.7 0.2 - - - -
188A PRO* 5.6 6.5 - - + -
633A ASP* 5.7 1.3 - - - -
715A SER 3.1 11.3 + - - +
716A ILE* 2.9 19.7 + - + +
718A TYR* 1.3 75.3 - - - +
720A ARG* 1.3 54.3 + - - -
721A GLN 3.3 8.7 + - - +
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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