Contacts of the helix formed by residues 595 - 605 (chain B) in PDB entry 3F8I
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 THR 595 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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591B PRO* 4.3 0.3 - - - +
592B GLU* 3.0 31.6 + - + +
594B TRP* 1.3 101.8 - - + +
596B ARG* 1.3 55.3 - - - +
597B GLU* 3.6 10.3 + - - +
598B GLY* 2.9 17.5 + - - -
599B LYS* 2.7 37.7 + - - +
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Residues in contact with ARG 596 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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595B THR* 1.3 73.1 - - - +
597B GLU* 1.3 62.1 + - - +
599B LYS* 3.3 9.8 + - - +
600B ASP* 3.1 34.5 + - - +
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Residues in contact with GLU 597 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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591B PRO* 3.9 23.8 - - + +
595B THR* 3.1 8.2 - - - +
596B ARG* 1.3 81.6 - - - +
598B GLY* 1.3 59.7 + - - +
600B ASP* 3.5 9.6 + - - +
601B ARG* 3.3 16.8 + - - +
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Residues in contact with GLY 598 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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591B PRO* 3.9 15.4 - - - +
592B GLU 3.2 24.7 - - - -
593B PRO* 4.2 6.6 - - - +
595B THR* 2.9 11.2 + - - -
597B GLU* 1.3 73.8 - - - +
599B LYS* 1.3 64.1 + - - +
600B ASP 3.1 1.8 - - - -
601B ARG* 3.5 3.8 + - - +
602B THR* 3.1 25.6 + - - -
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Residues in contact with LYS 599 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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593B PRO 3.6 13.0 - - - +
594B TRP* 3.6 26.6 + - - +
595B THR 2.7 22.7 + - - +
596B ARG* 3.9 8.6 - - - +
598B GLY* 1.3 72.3 - - - +
600B ASP* 1.3 62.0 + - - +
602B THR* 3.7 7.3 + - - -
603B ARG* 3.3 35.9 + - - +
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Residues in contact with ASP 600 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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596B ARG* 3.1 21.4 + - - +
597B GLU* 3.5 12.7 - - + +
598B GLY 3.1 0.2 - - - -
599B LYS* 1.3 76.6 - - - +
601B ARG* 1.3 61.4 + - - +
603B ARG* 2.8 32.7 + - - +
604B GLN* 2.8 32.0 + - - +
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Residues in contact with ARG 601 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430B PRO* 3.9 17.0 - - - +
431B VAL* 3.0 42.2 + - - +
590B GLU* 2.6 41.1 + - - +
591B PRO* 4.0 22.6 + - + -
597B GLU 3.3 10.6 + - - +
598B GLY 3.9 6.3 - - - +
599B LYS 3.4 0.2 - - - -
600B ASP* 1.3 78.1 - - - +
602B THR* 1.3 58.1 + - - +
604B GLN* 3.2 12.0 + - - +
605B LEU* 2.9 58.6 + - + +
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Residues in contact with THR 602 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431B VAL 4.8 1.8 + - - -
432B GLY* 4.4 17.0 - - - +
434B MET* 4.5 10.8 - - + -
593B PRO* 4.5 8.1 + - - +
598B GLY 3.1 16.4 + - - -
599B LYS* 3.9 8.2 - - - -
600B ASP 3.2 0.2 - - - -
601B ARG* 1.3 79.6 - - - +
603B ARG* 1.3 56.7 - - - +
605B LEU 3.6 0.5 + - - -
606B GLY* 3.1 5.4 + - - -
607B LEU* 3.1 59.0 + - + +
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Residues in contact with ARG 603 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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599B LYS* 3.3 23.1 + - - +
600B ASP* 2.8 37.8 + - - +
602B THR* 1.3 78.7 - - - +
604B GLN* 1.3 65.3 + - - +
606B GLY* 3.0 13.9 + - - -
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Residues in contact with GLN 604 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600B ASP* 2.8 14.3 + - - +
601B ARG* 3.5 17.6 - - - +
603B ARG* 1.3 78.5 - - - +
605B LEU* 1.3 71.1 + - + +
606B GLY 3.2 0.6 + - - -
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Residues in contact with LEU 605 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430B PRO* 4.2 17.0 - - + -
601B ARG* 2.9 56.9 + - + +
604B GLN* 1.3 89.0 - - + +
606B GLY* 1.3 63.7 + - - +
607B LEU* 3.0 27.4 + - + +
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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