Contacts of the helix formed by residues 708 - 716 (chain C) in PDB entry 6CIM
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 708 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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599C CYS 4.6 2.2 + - - -
600C ASP* 3.5 7.5 - - - +
662C GLU* 4.6 0.3 - - - +
707C TYR* 1.3 72.9 - - - +
709C GLU* 1.3 68.6 + - - +
710C LYS* 4.5 6.0 - - - +
711C LEU* 3.4 21.5 + - - +
712C VAL* 3.0 17.2 + - - +
1102C MN 2.1 35.7 + - - -
43G A 5.3 3.5 + - - -
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Residues in contact with GLU 709 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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707C TYR 4.6 0.2 - - - -
708C ASP* 1.3 75.8 - - - +
710C LYS* 1.3 64.8 + - - +
712C VAL* 3.1 8.4 + - - +
713C ARG* 2.9 61.9 + - + +
721C SER* 3.7 16.5 + - - +
726C ILE 4.2 1.9 - - - +
728C THR* 4.3 7.6 - - + +
934C ASN* 2.8 43.5 + - - +
935C TYR* 5.2 10.1 - - + +
938C LYS* 3.6 20.0 + - - +
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Residues in contact with LYS 710 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662C GLU* 3.3 34.0 + - - +
663C SER* 3.3 24.2 + - - -
708C ASP* 3.3 8.1 + - - +
709C GLU* 1.3 77.5 - - - +
711C LEU* 1.3 58.7 + - - +
713C ARG* 3.5 5.4 + - - +
714C GLU* 3.0 50.8 + - - +
721C SER* 4.6 13.9 + - - +
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Residues in contact with LEU 711 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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599C CYS* 3.3 51.6 - - + +
600C ASP* 3.9 9.4 - - - +
601C GLY 4.8 0.4 - - - +
620C VAL* 5.4 0.9 - - + -
662C GLU* 3.8 38.8 + - + +
668C LEU* 4.5 8.5 - - + -
707C TYR* 4.2 12.3 - - + -
708C ASP* 3.0 18.5 + - - +
710C LYS* 1.3 76.9 - - - +
712C VAL* 1.3 66.9 + - - +
714C GLU* 3.7 6.9 - - + +
715C VAL* 3.0 42.5 + - + +
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Residues in contact with VAL 712 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
707C TYR* 3.3 37.6 - - + +
708C ASP 3.0 9.1 + - - +
709C GLU* 3.4 9.9 - - - +
711C LEU* 1.3 76.9 - - - +
713C ARG* 1.3 64.4 + - - +
715C VAL* 3.4 7.5 - - - +
716C GLU* 2.9 30.4 + - + +
718C LEU* 5.5 0.9 - - + -
728C THR* 4.0 30.1 - - + +
787C THR* 3.9 20.4 - - - +
789C PRO* 4.1 18.6 - - + -
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Residues in contact with ARG 713 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709C GLU* 2.9 43.9 + - + +
710C LYS* 3.8 4.7 - - - +
712C VAL* 1.3 72.8 - - - +
714C GLU* 1.3 62.9 + - - +
717C GLY 3.5 1.0 + - - -
718C LEU* 3.1 53.8 + - + +
719C GLU 2.6 31.3 + - - +
720C ALA* 4.0 1.9 - - - +
721C SER* 3.9 32.1 + - - +
723C SER* 4.2 10.5 - - - -
725C TYR* 2.4 31.9 + - - +
726C ILE* 3.4 17.8 + - - +
727C CYS 4.8 0.8 + - - -
728C THR* 3.6 21.4 - - + +
934C ASN* 5.4 0.2 - - - -
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Residues in contact with GLU 714 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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662C GLU 3.4 18.9 - - - +
663C SER* 3.8 13.0 + - - +
665C HIS* 3.0 54.1 + - + +
668C LEU* 5.0 4.8 - - + +
710C LYS* 3.0 40.5 + - - +
711C LEU* 3.7 12.1 - - + +
712C VAL 3.2 0.2 - - - -
713C ARG* 1.3 80.9 - - - +
715C VAL* 1.3 64.1 + - + +
716C GLU 3.5 0.3 + - - -
717C GLY* 3.7 7.4 + - - -
718C LEU 5.0 1.1 - - - -
781C ALA* 5.9 0.2 - - - +
782C LYS 5.4 0.9 - - - +
784C PHE* 4.9 0.5 - - - -
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Residues in contact with VAL 715 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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668C LEU* 4.7 6.5 - - + -
672C LEU* 6.0 0.7 - - + -
707C TYR* 4.6 6.1 - - + -
711C LEU* 3.0 36.6 + - + +
712C VAL* 3.4 6.7 - - - +
714C GLU* 1.3 77.1 - - - +
716C GLU* 1.3 60.2 + - - +
717C GLY 3.4 0.9 - - - -
783C PRO* 3.5 0.4 - - - +
784C PHE* 3.0 52.9 + - + -
785C ILE* 3.3 32.3 + - + +
787C THR* 3.5 28.5 - - + -
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Residues in contact with GLU 716 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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712C VAL* 2.9 23.3 + - + +
714C GLU 3.3 0.2 - - - -
715C VAL* 1.3 76.3 - - - +
717C GLY* 1.3 61.7 + - - +
718C LEU* 3.2 14.5 + - + +
749C SER* 5.1 1.0 - - - -
750C HIS* 2.5 45.0 + - - +
753C ASN* 3.6 27.0 + - - +
779C VAL* 4.5 0.5 - - - +
783C PRO* 3.3 20.2 - - - +
785C ILE 3.2 15.8 - - - +
786C GLU* 4.5 0.2 - - - -
787C THR* 3.0 38.8 + - + +
789C PRO* 4.8 3.3 - - - +
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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