Contacts of the helix formed by residues 411 - 417 (chain D) in PDB entry 6CCV
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 GLY 411 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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404D ASP 4.9 1.8 - - - -
405D LEU* 3.1 15.9 - - - -
406D LEU 3.7 5.4 - - - -
407D LYS 3.4 17.3 + - - -
408D GLY 3.2 9.5 + - - -
409D LYS 3.4 0.2 - - - -
410D GLN* 1.3 77.8 - - - +
412D ARG* 1.3 63.6 + - - -
413D PHE 3.4 1.8 - - - -
414D ARG 4.4 1.1 - - - -
415D GLN* 2.8 29.3 + - - +
416D ASN* 4.2 2.0 - - - -
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Residues in contact with ARG 412 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1043C ILE* 3.0 37.1 - - - +
1044C THR* 3.9 19.2 - - - +
1111C SER* 5.6 7.2 - - - +
1114C VAL* 4.8 9.3 - - - +
1115C LEU* 4.3 20.6 - - + -
1118C GLU* 3.1 36.1 + - - +
405D LEU* 2.9 30.7 + - - +
406D LEU* 3.8 3.5 + - - -
411D GLY* 1.3 72.5 - - - -
413D PHE* 1.3 55.0 + - + +
416D ASN* 2.9 42.0 + - - +
417D LEU* 2.7 41.3 + - + +
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Residues in contact with PHE 413 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1115C LEU* 3.9 35.2 - - + -
1119C LEU* 5.6 2.9 - - + -
406D LEU* 3.2 49.8 - - + +
408D GLY 5.9 0.2 - - - +
411D GLY 3.4 0.4 - - - -
412D ARG* 1.3 77.6 - - + +
414D ARG* 1.3 60.5 + - + +
417D LEU* 3.6 10.5 - - + -
418D LEU* 2.5 37.5 + - + -
1221D TRP* 6.6 0.2 - + - -
1222D LEU* 4.6 7.2 - - + -
1225D ALA* 4.4 10.1 - - + -
1226D SER* 3.4 48.9 - - - +
1230D THR* 4.0 20.0 - - + -
1234D LEU* 5.5 2.9 - - + -
1254D ILE* 4.8 7.2 - - + -
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Residues in contact with ARG 414 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1058C ARG* 2.9 19.9 + - - -
1061C GLU* 4.0 17.1 + - - +
1204C EDO 4.4 7.1 + - - -
408D GLY 3.5 21.6 + - - +
409D LYS* 3.4 45.1 - - + +
411D GLY 4.0 2.2 + - - -
413D PHE* 1.3 82.4 - - + +
415D GLN* 1.3 60.3 + - - +
418D LEU* 4.4 11.2 - - + +
419D GLY 3.8 7.4 + - - -
874D ARG* 2.7 59.7 - - - +
1226D SER 4.5 5.6 - - - +
1227D PHE 5.2 0.9 + - - -
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Residues in contact with GLN 415 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1046C GLN* 4.5 2.0 + - - +
1058C ARG* 3.0 31.3 + - - +
409D LYS* 3.8 7.5 + - - +
410D GLN* 3.5 35.6 + - - +
411D GLY 2.8 20.2 + - - +
414D ARG* 1.3 78.4 - - - +
416D ASN* 1.3 73.4 + - - +
419D GLY 2.9 13.5 - - - +
420D LYS* 4.1 1.6 - - - -
375F ASP* 5.1 8.9 + - - -
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Residues in contact with ASN 416 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1044C THR* 3.8 14.2 - - - +
1046C GLN* 2.9 36.9 + - - +
1111C SER* 3.3 16.4 + - - -
410D GLN 4.6 2.0 + - - -
411D GLY 3.6 11.5 + - - -
412D ARG* 2.9 56.0 + - + +
415D GLN* 1.3 87.0 - - - +
417D LEU* 1.3 57.8 + - + +
419D GLY 3.2 6.5 - - - -
420D LYS* 3.2 13.3 - - - -
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Residues in contact with LEU 417 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1080C LEU* 4.5 10.0 - - - +
1111C SER* 2.9 32.3 - - - +
1112C PHE* 4.0 7.2 - - - +
1115C LEU* 3.6 39.5 - - + -
412D ARG* 2.7 26.8 + - + +
413D PHE* 3.2 13.5 - - + +
416D ASN* 1.3 74.8 - - - +
418D LEU* 1.3 69.4 + - + +
419D GLY* 3.2 3.7 + - - +
420D LYS* 4.1 11.4 + - - +
1253D VAL* 4.6 7.4 - - - +
1254D ILE* 3.4 39.7 - - + +
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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