Contacts of the helix formed by residues 515 - 522 (chain B) in PDB entry 4CCN
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 515 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192B LEU 4.1 7.6 - - - +
193B ASN* 3.7 34.1 - - - +
195B ILE 4.2 2.7 - - - +
201B ARG* 3.5 31.4 - - - +
513B VAL 5.2 0.7 - - - +
514B LEU* 1.3 77.5 - - - +
516B ASP* 1.3 66.0 + - - +
517B ARG* 3.4 7.3 + - - +
518B GLU* 2.8 42.3 + - - +
519B ARG* 3.1 21.2 + - - +
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Residues in contact with ASP 516 (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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193B ASN* 2.6 25.2 + - - +
515B THR* 1.3 75.9 - - - +
517B ARG* 1.3 58.1 + - - +
519B ARG* 3.6 9.5 + - - +
520B ALA* 2.9 31.2 + - - +
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Residues in contact with ARG 517 (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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193B ASN* 5.0 4.0 + - - +
196B PRO* 3.9 34.1 + - - +
515B THR* 3.2 9.3 + - - +
516B ASP* 1.3 76.8 - - - +
518B GLU* 1.3 69.2 + - - +
520B ALA* 3.2 5.8 + - - +
521B LEU* 2.9 62.0 + - + +
549B HIS* 5.3 6.3 + - - -
605B PHE* 4.3 21.0 - - - -
633B LEU* 5.3 6.1 - - - +
635B LYS 5.2 2.2 + - - -
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Residues in contact with GLU 518 (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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196B PRO 3.9 5.6 - - - +
201B ARG* 2.9 31.5 + - - +
514B LEU* 3.3 6.3 - - + -
515B THR* 2.8 39.9 + - - +
517B ARG* 1.3 79.1 - - + +
519B ARG* 1.3 58.4 + - - +
521B LEU* 3.0 3.3 + - - +
522B SER* 2.8 33.9 + - - -
551B LEU* 3.4 34.1 - - + +
552B GLN* 3.2 21.2 + - - +
602B TYR* 4.3 1.2 + - - -
633B LEU* 4.2 17.3 - - + -
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Residues in contact with ARG 519 (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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513B VAL* 5.7 0.8 - - - +
514B LEU* 3.4 52.4 + - + +
515B THR 3.1 15.1 + - - +
516B ASP* 3.6 10.9 + - - +
518B GLU* 1.3 78.2 - - - +
520B ALA* 1.3 62.9 + - - +
522B SER* 3.0 23.7 + - - -
524B TYR* 4.2 13.3 - - - +
525B GLY* 3.0 26.2 + - - +
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Residues in contact with ALA 520 (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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516B ASP 2.9 18.8 + - - +
517B ARG* 3.2 6.3 + - - +
519B ARG* 1.3 76.2 - - - +
521B LEU* 1.3 65.8 + - + +
522B SER 3.5 2.3 + - - +
525B GLY* 4.3 17.4 - - - +
526B LEU* 5.7 0.7 - - - +
527B PRO* 5.8 0.9 - - - +
637B PRO* 4.3 13.0 - - - +
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Residues in contact with LEU 521 (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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517B ARG* 2.9 56.9 + - + +
518B GLU 3.4 3.8 - - - +
520B ALA* 1.3 81.7 - - + +
522B SER* 1.3 59.6 + - - +
627B TYR* 3.7 8.2 + - - -
633B LEU* 3.6 17.9 - - + -
634B THR* 3.3 49.8 + - - +
635B LYS 4.0 6.7 - - - +
636B MET* 3.7 4.7 - - - -
637B PRO* 3.5 34.5 - - + -
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Residues in contact with SER 522 (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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514B LEU* 4.1 0.3 - - - +
518B GLU 2.8 13.3 + - - -
519B ARG* 3.0 17.4 + - - +
520B ALA 4.5 0.7 - - - +
521B LEU* 1.3 81.5 - - - +
523B VAL* 1.3 66.1 + - - +
524B TYR* 2.9 26.3 + - - -
525B GLY* 2.9 12.6 + - - -
526B LEU* 3.4 7.8 + - - +
551B LEU* 3.6 22.9 - - - -
627B TYR* 3.5 7.7 + - - -
630B GLY* 5.5 0.2 - - - -
632B LEU 4.1 9.6 - - - -
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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