Contacts of the helix formed by residues 448 - 466 (chain A) in PDB entry 1GC5
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 448 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A ILE* 4.1 20.6 - - - +
382A LYS* 3.4 17.8 - - - +
447A VAL* 1.3 81.7 - - - +
449A ILE* 1.3 55.4 + - - +
450A GLY 3.5 1.6 - - - -
451A ASP* 3.6 14.2 + - - +
452A THR* 2.4 34.0 + - - -
470A ADP 5.2 0.2 - - - -
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Residues in contact with ILE 449 (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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379A ALA* 3.9 17.7 - - + +
382A LYS* 4.4 11.2 - - + -
383A ALA* 3.6 28.3 - - + -
446A THR* 3.6 42.6 - - - +
447A VAL 3.6 2.6 + - - -
448A GLY* 1.3 73.6 - - - +
450A GLY* 1.3 61.0 + - - +
452A THR* 2.9 10.0 + - - -
453A ILE* 2.9 33.1 + - + +
470A ADP 3.1 50.0 + - + +
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Residues in contact with GLY 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A GLU* 4.0 2.2 - - - +
352A HIS* 4.6 6.9 - - - -
448A GLY 3.5 0.2 - - - -
449A ILE* 1.3 79.3 - - - +
451A ASP* 1.3 61.5 + - - +
453A ILE* 3.5 9.6 + - - +
454A SER* 3.2 25.3 + - - -
470A ADP 3.3 41.6 + - - -
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Residues in contact with ASP 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A GLN* 3.5 48.8 + - - +
124A ILE* 4.1 21.9 - - + +
125A MET* 4.0 18.8 - - + +
128A LEU* 5.4 0.2 - - - -
279A GLU* 3.9 13.7 - - - +
447A VAL 5.2 0.5 - - - +
448A GLY* 3.6 13.4 + - - +
449A ILE 3.2 0.6 - - - -
450A GLY* 1.3 74.9 - - - +
452A THR* 1.3 59.3 + - - +
454A SER* 4.2 0.2 - - - -
455A SER* 2.5 37.1 + - - -
470A ADP 5.2 5.6 + - - -
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Residues in contact with THR 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ILE* 5.2 2.5 - - - +
128A LEU* 3.6 28.4 - - + +
375A ALA 5.3 0.4 - - - -
378A ALA* 4.0 34.9 - - + +
379A ALA* 4.3 4.0 - - - +
382A LYS* 3.7 19.4 - - + +
388A LEU* 5.0 0.9 - - + -
448A GLY 2.4 26.0 + - - -
449A ILE* 2.9 10.9 + - - -
451A ASP* 1.3 79.4 - - - +
453A ILE* 1.3 57.2 + - - +
455A SER* 3.9 3.4 - - - -
456A SER* 2.7 34.8 + - - -
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Residues in contact with ILE 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A HIS* 3.7 20.8 - - + -
352A HIS* 4.0 18.6 - - + +
357A TYR* 3.2 35.0 - - + +
375A ALA* 3.3 27.7 - - - +
379A ALA* 3.6 11.7 - - + -
449A ILE* 2.9 18.2 + - + +
450A GLY* 3.6 7.0 - - - +
451A ASP 3.2 0.2 - - - -
452A THR* 1.3 76.5 - - - +
454A SER* 1.3 62.0 + - - +
457A ALA* 3.4 9.4 + - - +
470A ADP 3.1 47.6 - - + +
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Residues in contact with SER 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A HIS* 3.7 15.8 + - - -
279A GLU* 3.1 39.6 + - - -
303A GLY* 4.0 8.5 - - - -
350A HIS* 4.3 11.5 + - - -
352A HIS* 4.3 12.8 + - - -
450A GLY 3.2 8.3 + - - -
453A ILE* 1.3 81.1 - - - +
455A SER* 1.3 64.8 + - - +
457A ALA* 4.2 1.2 - - - +
458A PHE* 3.1 26.7 + - - +
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Residues in contact with SER 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A MET* 3.8 19.9 - - - +
128A LEU* 4.1 8.8 - - - +
129A LEU* 4.2 12.7 - - - +
238A ILE* 3.7 28.5 - - - +
279A GLU* 4.8 0.4 + - - -
451A ASP 2.5 26.0 + - - -
452A THR* 3.6 4.9 + - - -
454A SER* 1.3 76.2 - - - +
456A SER* 1.3 59.1 + - - +
458A PHE* 4.5 0.4 - - - -
459A VAL* 2.9 37.1 + - - +
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Residues in contact with SER 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A LEU* 3.8 5.2 - - - +
133A TYR* 2.6 40.5 + - - -
374A PHE* 3.9 8.4 - - - -
375A ALA* 4.0 19.3 - - - -
378A ALA* 3.9 4.1 - - - +
452A THR 2.7 24.4 + - - -
455A SER* 1.3 77.0 + - - +
457A ALA* 1.3 52.3 + - - +
459A VAL* 4.9 0.7 - - - -
460A SER* 2.7 39.2 + - - -
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Residues in contact with ALA 457 (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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348A ARG* 3.8 11.7 - - - +
350A HIS* 3.8 19.1 - - + +
371A ALA* 3.4 22.8 - - + +
372A LEU* 4.2 2.9 - - + -
375A ALA* 3.6 13.2 - - + +
453A ILE 3.4 15.6 + - - +
455A SER 3.4 0.2 - - - -
456A SER* 1.3 76.5 - - - +
458A PHE* 1.3 61.6 + - - +
460A SER* 3.8 0.2 - - - -
461A GLU* 2.9 34.8 + - - +
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Residues in contact with PHE 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A LEU* 3.9 25.1 - - + -
237A ALA 3.8 10.8 - - - -
238A ILE* 3.8 19.1 - - + -
275A LYS* 3.6 29.8 - - + -
276A SER 4.4 1.1 - - - -
277A HIS* 3.7 37.9 - - + -
300A THR* 5.4 3.4 - - + -
301A SER* 4.0 12.1 - - - -
348A ARG* 3.7 29.7 - - - +
454A SER 3.1 18.8 + - - +
455A SER* 3.9 2.0 - - - +
457A ALA* 1.3 80.8 - - - +
459A VAL* 1.3 68.3 + - + +
461A GLU* 3.9 2.2 - - - +
462A PHE* 3.3 20.5 + - + +
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Residues in contact with VAL 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ILE* 4.8 3.6 - - + -
30A VAL* 3.9 17.4 - - + +
33A VAL* 4.6 5.4 - - + -
129A LEU* 4.2 24.7 - - + -
133A TYR* 5.5 1.1 - - + -
135A ILE* 3.4 33.0 - - + -
236A LEU* 4.0 16.2 - - + -
238A ILE* 4.3 4.3 - - + -
455A SER 2.9 24.2 + - - +
456A SER* 4.5 1.8 - - - +
458A PHE* 1.3 89.2 - - + +
460A SER* 1.3 63.9 + - - +
462A PHE* 3.2 6.4 + - - +
463A GLY 3.1 17.3 + - - -
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Residues in contact with SER 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ALA* 4.4 11.4 - - - -
26A ALA* 4.4 0.7 - - - +
27A ILE* 3.9 27.5 - - - +
371A ALA* 3.6 17.0 - - - +
374A PHE* 4.0 13.5 - - - +
456A SER 2.7 23.2 + - - -
457A ALA 3.5 2.9 + - - -
459A VAL* 1.3 75.2 - - - +
461A GLU* 1.3 69.7 + - - +
463A GLY* 3.2 2.4 + - - +
464A MET* 3.0 30.4 + - - +
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Residues in contact with GLU 461 (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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348A ARG* 2.9 28.4 + - - -
363A TYR* 2.5 33.8 + - - -
367A GLU 3.9 15.5 - - - +
368A VAL* 3.4 30.0 - - + +
371A ALA* 3.4 13.4 - - + +
457A ALA 2.9 21.4 + - - +
458A PHE* 3.9 3.6 - - - +
460A SER* 1.3 76.6 + - - +
462A PHE* 1.3 57.9 + - - +
464A MET* 3.2 7.8 + - - +
465A ARG* 2.9 36.8 + - + +
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Residues in contact with PHE 462 (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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30A VAL* 4.2 8.5 - - + -
235A GLU* 3.6 35.7 - - + -
236A LEU* 3.4 41.7 - - + -
275A LYS* 3.8 22.2 - - + -
458A PHE* 3.3 12.3 + - + +
459A VAL 3.2 8.4 + - - +
460A SER 3.2 0.4 - - - -
461A GLU* 1.3 78.8 - - - +
463A GLY* 1.3 58.2 - - - +
465A ARG* 3.7 6.4 - - + +
466A LYS* 2.7 59.4 + - + +
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Residues in contact with GLY 463 (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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26A ALA* 3.5 23.4 - - - +
27A ILE* 5.5 0.2 - - - -
29A ASN* 3.7 14.5 + - - -
30A VAL* 4.0 15.3 - - - -
459A VAL 3.1 11.1 + - - -
460A SER* 3.2 3.3 + - - -
462A PHE* 1.3 76.7 - - - +
464A MET* 1.3 61.3 + - - +
466A LYS* 3.4 10.6 - - - +
467A ARG 3.2 13.7 + - - -
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Residues in contact with MET 464 (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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22A ASN* 4.1 26.9 - - + +
23A ALA* 4.3 5.6 - - + -
26A ALA* 3.3 20.6 - - + -
367A GLU* 3.2 51.1 - - + +
370A ASP* 3.9 17.3 - - + +
371A ALA* 3.4 26.2 - - + +
460A SER* 3.0 25.7 + - - +
461A GLU* 3.5 3.4 - - - +
463A GLY* 1.3 75.2 - - - +
465A ARG* 1.3 58.5 + - - +
467A ARG* 2.9 24.9 + - - +
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Residues in contact with ARG 465 (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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363A TYR* 3.3 52.9 - - - +
364A ARG 2.6 29.3 + - - +
367A GLU* 3.7 31.7 + - + +
368A VAL* 5.2 1.8 - - - +
461A GLU* 2.9 25.2 + - + +
462A PHE* 3.9 7.9 - - + +
464A MET* 1.3 73.1 - - - +
466A LYS* 1.3 64.0 + - - +
467A ARG* 2.5 22.3 + - - +
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Residues in contact with LYS 466 (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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29A ASN* 2.7 37.8 + - + +
31A LYS* 3.7 15.4 - - - +
235A GLU* 2.7 39.6 + - - -
462A PHE* 2.7 34.4 + - + +
463A GLY* 3.4 8.7 - - - +
465A ARG* 1.3 76.4 - - - +
467A ARG* 1.3 74.2 + - - +
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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
------------------------------------------------------------
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