Contacts of the helix formed by residues 629 - 638 (chain C) in PDB entry 3KMR
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 HIS 629 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258A ILE* 4.0 31.9 - - + +
262A LYS* 4.1 15.8 - - + +
412A GLU* 3.2 44.0 - - + +
630C LYS* 1.3 61.0 + - - +
632C LEU* 4.2 10.3 - - + -
633C HIS* 2.8 52.7 + - - +
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Residues in contact with LYS 630 (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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412A GLU* 3.4 7.4 + - - +
629C HIS* 1.3 76.9 - - - +
631C ILE* 1.3 66.5 + - + +
633C HIS* 3.4 6.6 + - - +
634C ARG* 3.0 23.1 + - - +
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Residues in contact with ILE 631 (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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237A ILE* 6.4 0.7 - - + -
408A PRO* 3.7 29.8 - - + -
409A LEU* 3.9 31.9 - - + +
412A GLU* 2.8 25.6 + - - +
630C LYS* 1.3 74.8 - - + +
632C LEU* 1.3 56.3 + - - +
634C ARG* 3.0 34.7 + - - +
635C LEU* 2.9 38.1 + - + +
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Residues in contact with LEU 632 (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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240A VAL* 3.7 31.2 - - + -
258A ILE* 3.9 42.8 - - + +
261A LEU* 4.4 11.4 - - + -
262A LYS* 4.5 4.7 - - + -
409A LEU* 4.6 3.1 - - + +
412A GLU* 2.9 19.1 + - - +
413A MET* 3.8 35.2 - - + -
629C HIS* 3.8 9.9 - - + +
631C ILE* 1.3 77.1 - - - +
633C HIS* 1.3 56.9 + - - +
635C LEU* 3.4 10.2 + - + +
636C LEU* 2.9 37.9 + - + +
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Residues in contact with HIS 633 (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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254A ILE* 3.5 32.3 - - + +
258A ILE* 3.5 18.6 - - + +
629C HIS* 2.8 42.1 + - + +
630C LYS* 3.6 6.2 - - - +
632C LEU* 1.3 71.6 - - - +
634C ARG* 1.3 62.7 + - - +
636C LEU* 3.3 8.1 + - + +
637C GLN* 3.2 22.3 + - - +
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Residues in contact with ARG 634 (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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630C LYS 3.0 12.4 + - - +
631C ILE* 3.0 44.3 + - - +
633C HIS* 1.3 77.8 - - - +
635C LEU* 1.3 72.7 + - - +
637C GLN* 3.2 9.3 + - - +
638C GLU* 3.0 41.0 + - - +
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Residues in contact with LEU 635 (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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237A ILE* 4.2 39.5 - - + +
240A VAL* 3.9 31.4 - - + -
241A GLU* 6.5 0.4 - - + -
244A LYS* 2.8 29.6 + - - -
409A LEU* 4.3 12.6 - - + -
631C ILE* 2.9 34.3 + - + +
632C LEU* 3.7 5.8 - - - +
634C ARG* 1.3 88.6 - - - +
636C LEU* 1.3 58.8 + - - +
638C GLU* 3.0 26.4 - - + +
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Residues in contact with LEU 636 (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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240A VAL* 3.9 14.8 - - + -
244A LYS* 3.8 25.0 - - + +
249A PHE* 4.3 3.1 - - + -
250A THR* 5.4 4.0 - - - +
254A ILE* 4.8 17.2 - - + +
257A GLN* 3.7 35.7 - - + +
258A ILE* 3.8 30.5 - - + -
261A LEU* 3.8 26.7 - - + -
632C LEU* 2.9 23.1 + - + +
633C HIS* 3.3 6.5 + - - +
634C ARG 3.3 0.2 - - - -
635C LEU* 1.3 76.1 - - - +
637C GLN* 1.3 61.7 + - - +
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Residues in contact with GLN 637 (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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244A LYS* 4.2 4.0 + - - +
633C HIS 3.2 12.8 + - - +
634C ARG* 3.7 10.5 - - - +
635C LEU 3.2 0.2 - - - -
636C LEU* 1.3 79.7 - - - +
638C GLU* 1.3 82.2 + - - +
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Residues in contact with GLU 638 (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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244A LYS* 3.6 13.2 - - - +
634C ARG* 3.0 30.9 + - - +
635C LEU* 3.0 47.3 - - - +
637C GLN* 1.3 91.6 + - - +
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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