Contacts of the helix formed by residues 405 - 416 (chain D) in PDB entry 3F7F
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 GLU 405 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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403D ASP* 3.8 16.4 - - - +
404D VAL* 1.3 87.7 - - + +
406D ARG* 1.3 59.4 + - - +
407D GLY 3.2 0.2 - - - -
408D PHE* 3.1 12.6 + - + +
409D CYS* 2.9 34.5 + - - -
437D ASN* 2.7 38.6 + - - +
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Residues in contact with ARG 406 (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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400D LYS* 3.5 46.9 - - - +
401D THR 3.6 23.6 - - - +
403D ASP* 3.4 28.2 + - + +
405D GLU* 1.3 79.7 - - - +
407D GLY* 1.3 56.8 + - - +
408D PHE 3.1 0.2 - - - -
409D CYS* 3.3 21.2 + - - +
410D ASN* 2.9 59.1 + - - +
669D ARG 5.5 4.2 + - - -
670D GLN* 3.8 23.4 - - - +
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Residues in contact with GLY 407 (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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403D ASP 3.4 6.8 + - - -
404D VAL 3.3 9.2 + - - -
405D GLU 3.2 0.6 - - - -
406D ARG* 1.3 78.1 - - - +
408D PHE* 1.3 58.6 + - - +
410D ASN* 3.8 13.4 - - - +
411D LEU* 2.9 35.8 + - - +
443D LEU* 4.1 13.7 - - - -
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Residues in contact with PHE 408 (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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404D VAL* 3.2 9.1 + - + -
405D GLU* 3.1 21.9 + - + +
407D GLY* 1.3 77.9 - - - +
409D CYS* 1.3 60.3 + - - +
410D ASN 3.2 0.2 - - - -
411D LEU* 3.4 5.4 + - + +
412D LYS* 2.9 38.7 + - + +
420D PHE* 3.6 25.0 - + - -
424D GLN* 3.3 28.5 - - - -
434D MET* 4.0 29.8 - - + -
442D TYR* 4.3 7.0 - + - -
443D LEU* 5.4 6.5 - - + -
446D LEU* 3.4 24.7 - - + -
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Residues in contact with CYS 409 (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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405D GLU* 2.9 19.4 + - - -
406D ARG* 3.7 26.0 - - - +
408D PHE* 1.3 75.3 - - - +
410D ASN* 1.3 60.1 + - - +
412D LYS* 3.9 6.0 - - - +
413D SER* 2.8 34.9 + - - -
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Residues in contact with ASN 410 (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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399D THR* 3.4 25.7 - - + +
400D LYS 2.9 28.0 + - - +
401D THR* 5.2 0.2 - - - +
406D ARG* 2.9 52.9 + - - +
407D GLY* 3.8 11.2 - - - +
408D PHE 3.2 0.2 - - - -
409D CYS* 1.3 76.1 - - - +
411D LEU* 1.3 56.1 + - + +
413D SER* 3.7 3.9 - - - -
414D ARG* 2.7 37.2 + - - +
669D ARG 5.7 2.9 - - - +
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Residues in contact with LEU 411 (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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407D GLY 2.9 25.9 + - - +
408D PHE* 3.9 5.8 - - + +
409D CYS 3.4 0.4 - - - -
410D ASN* 1.3 74.6 - - + +
412D LYS* 1.3 59.0 + - - +
414D ARG* 4.1 10.1 - - - +
415D TYR* 2.7 49.3 + - + +
420D PHE* 4.2 4.5 - - + -
443D LEU* 4.4 20.4 - - + -
446D LEU* 4.4 18.4 - - + -
447D GLU* 3.8 29.6 - - + +
450D LEU* 3.6 29.8 - - + -
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Residues in contact with LYS 412 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16D GLU* 5.4 6.8 - - - +
408D PHE* 2.9 26.7 + - + +
409D CYS* 3.9 5.8 - - - +
411D LEU* 1.3 75.3 - - - +
413D SER* 1.3 58.9 + - - +
416D GLY* 3.0 30.7 + - - -
417D THR* 3.7 23.1 + - - +
420D PHE* 3.7 45.4 - - + -
421D GLU* 4.9 8.1 + - - -
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Residues in contact with SER 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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13D GLN* 3.9 8.7 + - - -
409D CYS 2.8 20.4 + - - -
410D ASN* 3.7 3.1 - - - -
412D LYS* 1.3 77.8 - - - +
414D ARG* 1.3 64.0 + - - +
415D TYR 3.5 0.2 + - - -
416D GLY* 4.0 1.6 + - - -
668D TYR 4.7 0.3 + - - -
669D ARG* 2.8 29.8 + - - +
670D GLN 4.7 5.3 - - - -
671D ASP* 4.9 1.7 + - - -
672D LYS* 3.2 25.2 + - - +
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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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13D GLN* 3.7 10.0 + - - -
387D VAL* 3.5 29.2 + - + +
388D ASP* 3.2 27.1 + - - +
391D SER* 2.7 41.6 + - - -
410D ASN 2.7 23.7 + - - +
411D LEU* 3.1 10.3 + - - +
413D SER* 1.3 76.4 + - - +
415D TYR* 1.3 102.0 + - + +
447D GLU* 5.3 5.3 + - - -
451D ARG* 5.9 2.0 - - - +
669D ARG* 6.5 0.2 - - - -
672D LYS* 4.1 10.7 + - - +
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Residues in contact with TYR 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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10D ASN* 5.3 6.4 + - - +
13D GLN* 4.4 5.5 + - - -
388D ASP* 5.5 0.4 - - - -
411D LEU* 2.7 37.0 + - + +
412D LYS 4.6 0.2 - - - +
414D ARG* 1.3 126.1 + - - +
416D GLY* 1.3 65.7 + - - +
419D ILE* 3.6 44.3 - - + +
420D PHE* 4.6 1.8 - - + +
447D GLU* 4.5 4.1 + - - -
450D LEU* 3.6 51.1 - - + +
451D ARG* 3.8 19.8 + - - +
454D LYS* 4.0 24.0 - - + -
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Residues in contact with GLY 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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10D ASN* 6.1 1.8 - - - -
13D GLN* 4.5 25.1 - - - -
412D LYS* 3.0 18.1 + - - -
413D SER 4.0 2.7 + - - -
414D ARG 3.7 1.0 - - - -
415D TYR* 1.3 80.6 - - - +
417D THR* 1.3 60.1 + - - -
418D GLN* 3.4 2.7 - - - -
419D ILE 3.4 1.3 + - - -
420D PHE* 3.0 27.6 + - - +
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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