Contacts of the helix formed by residues 661 - 671 (chain C) in PDB entry 4MNE
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 661 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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659C ILE* 3.6 2.4 - - - +
660C ASN* 1.3 82.5 - - - +
662C ARG* 1.3 65.3 + - - +
663C ASP* 3.1 19.1 + - - +
664C GLN* 3.4 31.3 + - + +
665C ILE* 3.1 25.9 + - - +
189D ARG* 5.5 0.2 - - - +
230D MET* 3.1 38.2 - - - +
234D ARG* 3.7 29.0 + - - +
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Residues in contact with ARG 662 (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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617C ILE* 4.1 15.9 - - + +
660C ASN 4.0 2.8 + - - -
661C ASN* 1.3 73.5 + - - +
663C ASP* 1.3 84.0 + - - +
665C ILE* 3.2 5.9 + - - +
666C ILE* 2.9 38.6 + - + +
78D ASN* 4.6 18.3 + - - +
79D GLY 6.0 0.2 - - - +
190D ASP* 5.4 6.9 + - - -
192D LYS* 5.9 3.0 - - - +
219D MET* 3.7 42.4 + - - +
220D ALA* 4.4 6.6 - - - +
222D SER* 3.4 31.1 + - - +
223D PHE 4.4 9.7 + - - +
225D GLY* 5.4 5.2 - - - +
230D MET* 6.0 4.0 - - + +
903D 573 5.3 4.2 - - - +
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Residues in contact with ASP 663 (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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661C ASN* 3.1 7.7 + - - +
662C ARG* 1.3 94.8 + - - +
664C GLN* 1.3 57.6 + - - +
666C ILE* 3.3 19.9 - - - +
667C PHE* 3.0 26.9 + - - +
225D GLY* 5.5 0.7 + - - -
227D ARG 4.3 2.8 - - - +
228D SER* 2.5 35.5 + - - +
229D TYR 4.9 0.2 + - - -
230D MET* 4.0 13.7 - - + +
235D LEU* 3.6 17.7 - - + -
310D ILE* 3.8 9.9 - - - +
314D LEU* 3.3 12.9 - - + +
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Residues in contact with GLN 664 (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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659C ILE* 3.9 30.9 - - + +
661C ASN* 3.3 32.7 + - + +
662C ARG 3.2 0.4 - - - -
663C ASP* 1.3 75.2 - - - +
665C ILE* 1.3 56.2 + - - +
667C PHE* 3.9 0.6 - - - +
668C MET* 2.8 62.3 + - - +
234D ARG 3.6 17.3 - - - +
235D LEU* 3.3 27.9 - - - +
237D GLY* 3.8 15.0 - - - -
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Residues in contact with ILE 665 (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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617C ILE* 3.8 30.7 - - + +
618C LEU* 4.3 9.9 - - + -
625C ILE* 6.0 1.3 - - + -
656C TYR* 3.8 36.3 - - + -
659C ILE* 3.6 34.5 - - + +
661C ASN 3.1 17.4 + - - +
662C ARG* 3.6 6.5 - - - +
664C GLN* 1.3 71.4 - - - +
666C ILE* 1.3 70.9 + - - +
669C VAL* 3.0 27.9 + - + +
674C LEU* 4.2 13.0 - - + -
220D ALA* 4.8 8.7 - - + -
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Residues in contact with ILE 666 (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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617C ILE* 3.7 28.0 - - + -
625C ILE* 3.4 38.2 - - + +
662C ARG* 2.9 27.4 + - + +
663C ASP* 3.3 27.4 - - - +
665C ILE* 1.3 78.8 - - - +
667C PHE* 1.3 65.0 + - - +
670C GLY* 3.1 15.9 + - - -
224D VAL* 4.7 13.5 - - + -
225D GLY 4.9 1.3 - - - +
310D ILE* 4.2 26.0 - - + -
311D PHE* 4.8 4.0 - - + -
314D LEU* 3.6 13.0 - - + -
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Residues in contact with PHE 667 (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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663C ASP 3.0 15.2 + - - +
664C GLN 3.9 0.9 - - - +
666C ILE* 1.3 80.2 - - - +
668C MET* 1.3 67.8 + - + +
670C GLY 3.4 0.2 + - - -
671C ARG* 2.9 61.4 + - + +
673C TYR* 4.7 8.3 - + - -
235D LEU* 3.6 28.3 - - + -
236D GLN* 4.3 12.8 - - + -
311D PHE* 3.5 15.4 - + - -
314D LEU* 3.5 31.4 - - + -
315D ASP* 4.0 15.0 - - + -
318D VAL* 3.8 34.8 - - + -
319D ASN* 5.2 0.7 - - - -
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Residues in contact with MET 668 (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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659C ILE* 5.0 2.9 - - + -
664C GLN* 2.8 55.3 + - - +
667C PHE* 1.3 76.8 - - + +
669C VAL* 1.3 58.6 + - - +
671C ARG* 4.4 2.9 - - - -
672C GLY 3.4 1.4 + - - -
673C TYR* 2.7 58.1 + - + +
674C LEU* 3.0 37.5 + - + -
235D LEU 4.0 10.8 - - - +
236D GLN* 4.3 15.0 - - - +
237D GLY* 5.5 0.9 - - - -
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Residues in contact with VAL 669 (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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620C MET 4.4 7.0 - - - +
622C PRO* 3.3 32.7 - - + +
625C ILE* 3.6 22.7 - - + -
640C TYR* 4.5 7.6 - - - +
656C TYR* 3.6 33.4 - - + +
665C ILE* 3.0 23.2 + - + +
668C MET* 1.3 75.5 - - - +
670C GLY* 1.3 63.2 + - - +
672C GLY* 3.3 10.9 + - - -
674C LEU* 3.8 29.1 - - + +
699C LYS* 6.0 0.2 - - - -
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Residues in contact with GLY 670 (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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622C PRO* 4.1 16.4 - - - -
625C ILE* 4.3 4.9 - - - +
626C ARG* 3.0 32.1 + - - -
666C ILE 3.1 12.0 + - - -
669C VAL* 1.3 74.5 - - - +
671C ARG* 1.3 59.9 + - - +
672C GLY 3.0 4.7 - - - -
311D PHE* 3.7 22.7 - - - -
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Residues in contact with ARG 671 (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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626C ARG* 5.2 2.2 - - - +
628C GLN* 5.9 0.6 + - - -
667C PHE* 2.9 42.4 + - + +
668C MET 4.0 1.6 - - - +
670C GLY* 1.3 75.4 + - - +
672C GLY* 1.3 58.6 + - - +
673C TYR* 3.4 50.9 + - + -
311D PHE* 3.6 20.1 - - - -
315D ASP* 3.3 23.1 + - - -
319D ASN* 4.4 8.7 - - - +
636F GLN* 5.1 9.5 - - - +
700F LYS* 5.8 2.6 + - - -
702F ASP* 3.3 52.9 + - - +
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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