Contacts of the helix formed by residues 408 - 420 (chain A) in PDB entry 1Q2L
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 ASP 408 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A LEU* 3.4 18.6 - - - +
132A GLU* 4.6 8.3 - - - +
406A THR* 2.9 29.2 + - + +
407A ARG* 1.3 75.7 - - - +
409A MET* 1.3 66.0 + - - +
410A ASP* 3.3 28.4 + - - +
411A TYR* 3.0 22.8 + - - +
412A VAL 3.3 5.4 + - - -
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Residues in contact with MET 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LEU* 3.7 7.0 - - - +
117A SER* 3.8 19.5 - - - +
118A HIS* 3.7 31.2 - - - +
119A ASN* 3.5 31.6 - - + +
130A TYR* 3.5 20.5 - - + -
131A LEU* 4.2 14.6 - - - +
132A GLU* 4.2 11.8 + - + +
408A ASP* 1.3 78.6 - - - +
410A ASP* 1.3 68.5 + - - +
412A VAL* 3.1 23.6 - - - +
413A GLU* 3.1 10.1 + - - +
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Residues in contact with ASP 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A TYR* 5.0 6.2 - - - -
408A ASP* 3.2 17.5 + - - +
409A MET* 1.3 86.4 - - - +
411A TYR* 1.3 57.0 + - - +
413A GLU* 3.2 12.6 + - + +
414A TRP* 2.8 30.3 + - - +
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Residues in contact with TYR 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ARG* 3.6 31.7 + - - -
44A TYR* 4.0 10.1 + - - -
58A VAL* 5.9 0.2 - - + -
67A LEU* 4.7 0.7 - - + -
236A TYR* 4.0 13.7 - + - -
406A THR 3.6 23.8 - - - +
407A ARG* 4.2 13.9 - - + -
408A ASP* 3.0 14.5 + - - +
410A ASP* 1.3 78.3 - - - +
412A VAL* 1.3 61.0 + - + +
414A TRP* 3.1 35.0 + + + +
415A LEU* 3.0 56.2 + - + +
428A LEU* 4.5 7.8 - - - +
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Residues in contact with VAL 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LEU* 3.3 47.8 - - + -
68A SER 3.9 17.5 - - - +
69A ALA* 3.8 12.4 - - + +
130A TYR* 4.3 2.5 - - + -
131A LEU 4.3 1.6 - - - +
234A VAL* 4.3 14.8 - - + +
236A TYR* 4.1 12.6 - - + -
408A ASP 3.3 2.4 + - - +
409A MET* 3.1 20.2 - - - +
411A TYR* 1.3 76.7 - - + +
413A GLU* 1.3 65.9 + - - +
415A LEU* 3.2 9.2 + - + +
416A ALA* 2.9 26.0 + - - +
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Residues in contact with GLU 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ALA* 4.6 3.4 - - - -
71A VAL* 4.9 0.2 - - - +
121A SER* 4.2 2.8 + - - -
126A ARG* 3.3 15.5 + - - -
128A ALA* 3.8 5.5 - - - +
130A TYR* 3.1 49.5 + - + -
409A MET 3.1 14.5 + - - +
410A ASP* 3.2 18.2 - - + +
412A VAL* 1.3 78.3 - - - +
414A TRP* 1.3 64.7 + - - +
416A ALA* 3.4 1.9 + - - +
417A ASP* 3.0 44.3 + - - +
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Residues in contact with TRP 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410A ASP 2.8 13.2 + - - +
411A TYR* 3.2 31.2 - + + +
413A GLU* 1.3 79.3 - - - +
415A LEU* 1.3 93.2 + - + +
417A ASP* 3.3 9.0 + - + +
418A THR* 2.9 39.2 + - + -
421A ARG* 5.8 1.2 - - - +
427A THR 4.3 8.7 - - - -
428A LEU* 4.3 20.4 - - + -
430A ALA* 6.0 1.3 - - + -
431A VAL* 4.3 33.1 - - + +
432A ASN* 5.8 0.2 - - - -
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Residues in contact with LEU 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A TYR* 5.7 0.2 - - + -
56A LEU* 4.4 8.7 - - + -
58A VAL* 4.7 9.0 - - + -
234A VAL* 4.1 27.4 - - + -
236A TYR* 5.2 0.7 - - + -
411A TYR* 3.0 47.4 + - + +
412A VAL* 3.2 10.1 + - + +
414A TRP* 1.3 103.7 - - + +
416A ALA* 1.3 61.9 + - - +
418A THR* 3.2 6.6 + - - -
419A MET* 3.1 26.3 + - - +
427A THR* 3.6 13.7 - - + +
428A LEU* 3.9 23.8 - - + -
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Residues in contact with ALA 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A ALA* 4.0 16.2 - - + -
71A VAL* 3.3 31.2 - - + +
232A LYS* 4.4 6.9 - - - +
234A VAL* 4.0 13.1 - - + +
412A VAL 2.9 16.7 + - - +
413A GLU* 3.8 2.9 - - - +
415A LEU* 1.3 76.7 - - - +
417A ASP* 1.3 62.7 + - - +
419A MET* 3.2 20.2 + - - +
420A ILE* 3.6 12.3 + - - +
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Residues in contact with ASP 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A VAL* 3.6 11.2 - - - +
125A TYR* 5.1 7.4 + - + +
126A ARG* 2.7 43.8 + - - -
413A GLU* 3.0 31.7 + - - +
414A TRP* 3.6 11.6 - - + +
416A ALA* 1.3 75.7 - - - +
418A THR* 1.3 62.8 + - - +
420A ILE* 3.0 27.7 - - + +
421A ARG* 3.6 14.4 - - - +
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Residues in contact with THR 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414A TRP* 2.9 33.3 + - + -
415A LEU* 3.2 8.0 + - - -
417A ASP* 1.3 77.5 - - - +
419A MET* 1.3 58.0 + - - +
421A ARG* 2.8 47.3 + - - +
422A VAL* 3.0 22.9 + - + +
427A THR* 3.6 21.0 + - - +
430A ALA* 3.5 23.6 - - + -
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Residues in contact with MET 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A VAL* 3.4 39.5 - - + +
56A LEU* 3.8 21.3 - - + +
232A LYS* 3.7 33.2 - - + -
233A ALA 3.6 20.6 - - - +
234A VAL* 3.7 19.3 - - - -
415A LEU 3.1 15.7 + - - +
416A ALA* 3.2 9.8 + - - +
418A THR* 1.3 77.2 - - - +
420A ILE* 1.3 58.8 + - - +
421A ARG 3.2 0.4 - - - -
422A VAL 3.5 16.5 - - - +
424A VAL* 4.3 8.0 + - + +
427A THR* 3.7 21.1 - - + +
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Residues in contact with ILE 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A VAL* 3.9 21.3 - - + -
73A PRO* 4.4 26.9 - - + -
125A TYR* 4.1 16.2 - - + +
126A ARG* 3.8 35.4 - - + -
230A LEU 5.0 0.4 - - - +
232A LYS* 3.6 25.4 - - + +
262A LYS* 4.5 18.8 + - - +
416A ALA 3.9 3.8 - - - +
417A ASP* 3.0 21.1 - - - +
419A MET* 1.3 77.1 - - - +
421A ARG* 1.3 63.8 + - + +
422A VAL 3.8 0.2 - - - -
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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