Contacts of the helix formed by residues 631 - 639 (chain G) in PDB entry 4JYH
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 LYS 631 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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405A GLU* 4.7 0.4 - - - -
629G ARG* 2.9 23.9 + - - +
630G HIS* 1.3 77.5 - - - +
632G ILE* 1.3 64.5 + - - +
633G LEU 3.8 0.4 - - - -
634G HIS* 4.5 10.8 - - - +
635G ARG* 3.4 21.8 + - - +
701G FLC 3.0 39.6 + - - +
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Residues in contact with ILE 632 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401A PRO* 3.3 38.4 - - + +
402A LEU* 3.8 30.1 - - + +
405A GLU* 3.8 7.4 + - - +
630G HIS* 3.7 2.1 - - + +
631G LYS* 1.3 75.9 - - - +
633G LEU* 1.3 70.1 + - - +
634G HIS 3.2 1.8 - - - -
635G ARG* 2.8 35.1 + - - +
636G LEU* 2.9 23.8 + - + +
701G FLC 3.1 32.1 - - + +
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Residues in contact with LEU 633 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A VAL* 3.7 31.2 - - + -
251A ILE* 3.6 38.6 - - + +
254A LEU* 4.2 10.3 - - + -
255A LYS* 4.2 7.6 - - + -
402A LEU* 4.2 10.5 - - + +
405A GLU* 3.1 31.0 + - - +
406A MET* 3.6 32.5 - - + -
632G ILE* 1.3 78.6 - - - +
634G HIS* 1.3 56.4 + - - +
636G LEU* 3.1 7.6 + - + +
637G LEU* 2.9 27.6 + - + +
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Residues in contact with HIS 634 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A ILE* 4.1 18.6 - - + +
251A ILE* 3.4 36.5 - - + +
405A GLU* 4.6 10.2 + - - -
630G HIS 4.8 9.7 + - - -
631G LYS* 4.3 8.2 + - - +
632G ILE 3.2 0.8 - - - -
633G LEU* 1.3 79.3 - - - +
635G ARG* 1.3 62.5 + - - +
637G LEU* 3.0 9.0 + - + +
638G GLN* 2.9 25.0 + - - +
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Residues in contact with ARG 635 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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631G LYS 3.4 14.8 + - - +
632G ILE* 2.8 29.7 + - - +
634G HIS* 1.3 74.6 - - - +
636G LEU* 1.3 68.7 + - + +
638G GLN* 3.4 9.6 + - + +
639G GLU 3.2 24.2 + - - +
701G FLC 2.9 40.7 + - - -
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Residues in contact with LEU 636 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A ILE* 4.1 34.3 - - + -
233A VAL* 4.1 22.5 - - + +
237A LYS* 2.8 23.6 + - - +
402A LEU* 3.8 33.7 - - + -
632G ILE* 2.9 29.1 + - + +
633G LEU* 3.4 8.7 - - - +
635G ARG* 1.3 82.5 - - + +
637G LEU* 1.3 61.2 + - - +
639G GLU* 3.1 10.3 + - - +
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Residues in contact with LEU 637 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A VAL* 4.5 3.8 - - + +
237A LYS* 3.1 40.2 + - + +
242A PHE* 4.4 3.1 - - + -
243A THR* 5.5 2.2 - - + +
247A ILE* 4.3 16.2 - - + -
250A GLN* 4.0 29.8 - - + +
251A ILE* 3.4 36.3 - - + +
254A LEU* 4.3 19.7 - - + -
633G LEU 2.9 12.4 + - - +
634G HIS* 3.3 11.0 - - + +
636G LEU* 1.3 76.7 - - - +
638G GLN* 1.3 62.5 + - - +
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Residues in contact with GLN 638 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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634G HIS 2.9 15.2 + - - +
635G ARG* 3.8 9.8 - - + +
636G LEU 3.3 0.2 - - - -
637G LEU* 1.3 75.6 - - - +
639G GLU* 1.3 80.3 + - - +
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Residues in contact with GLU 639 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A LYS* 3.5 15.7 - - - +
635G ARG* 3.2 14.9 + - - +
636G LEU* 3.1 16.7 + - - +
637G LEU 3.1 2.4 - - - -
638G GLN* 1.3 85.3 - - - +
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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