Contacts of the helix formed by residues 413 - 429 (chain D) in PDB entry 2GL7
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 413 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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375D GLN* 4.4 14.2 - - - +
379D GLN* 4.4 5.5 + - - -
411D SER* 3.1 13.6 + - - +
412D ASP* 1.3 85.5 - - - +
414D ILE* 1.3 58.2 + - - +
415D ASN* 3.1 23.7 + - - +
416D VAL* 3.0 38.8 + - + +
417D VAL* 3.2 10.6 + - - +
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Residues in contact with ILE 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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412D ASP 3.7 4.4 + - - +
413D ASP* 1.3 72.6 + - - +
415D ASN* 1.3 70.1 + - - +
417D VAL* 3.8 23.6 - - + -
418D THR* 2.7 32.3 + - - +
450D THR* 5.6 0.4 - - + -
453D ARG* 4.3 30.9 - - + +
454D ALA* 5.5 2.5 - - - -
457D ARG* 5.0 11.9 - - - +
460D ILE* 3.3 33.2 - - + -
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Residues in contact with ASN 415 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379D GLN* 4.1 19.9 - - - +
383D TRP* 5.7 6.2 - - + -
413D ASP* 3.1 11.8 + - - +
414D ILE* 1.3 86.0 - - - +
416D VAL* 1.3 64.7 + - - +
418D THR* 3.3 8.5 + - - -
419D CYS* 3.1 24.3 + - - +
457D ARG* 4.6 9.9 + - - -
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Residues in contact with VAL 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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378D VAL* 5.4 7.6 - - + -
379D GLN* 3.9 15.2 + - - +
382D LEU* 4.0 25.9 - - + +
408D LEU* 3.9 35.0 - - + +
411D SER* 4.0 12.8 - - - +
413D ASP* 3.0 32.1 + - + +
415D ASN* 1.3 76.0 - - - +
417D VAL* 1.3 63.0 + - - +
419D CYS* 3.2 4.9 + - - +
420D ALA* 3.0 21.5 + - - +
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Residues in contact with VAL 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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408D LEU 3.7 14.6 - - - +
409D LEU* 3.3 27.6 - - + +
411D SER* 3.8 10.1 - - - +
413D ASP 3.2 8.6 + - - +
414D ILE* 3.7 20.2 - - + +
415D ASN 3.3 0.2 - - - -
416D VAL* 1.3 75.3 - - - +
418D THR* 1.3 58.7 + - - +
420D ALA* 3.3 5.1 + - - +
421D ALA* 2.9 27.5 + - - +
450D THR* 3.5 37.5 - - + +
453D ARG* 3.8 19.1 - - - +
460D ILE* 4.7 0.9 - - + -
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Residues in contact with THR 418 (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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386D ARG* 4.2 16.1 + - - +
414D ILE* 2.7 22.5 + - - +
415D ASN* 3.5 8.8 + - - -
416D VAL 3.2 0.2 - - - -
417D VAL* 1.3 77.4 - - - +
419D CYS* 1.3 62.7 + - - +
421D ALA* 3.3 7.5 + - - +
422D GLY* 3.2 18.0 + - - -
457D ARG* 4.8 0.9 + - - -
459D ASP* 3.9 33.7 + - + +
460D ILE* 3.3 27.3 - - + +
463D PRO* 4.6 3.1 - - + +
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Residues in contact with CYS 419 (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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379D GLN* 4.2 7.6 - - - -
382D LEU* 4.0 36.3 - - + -
383D TRP* 3.8 27.8 - - - -
386D ARG* 3.7 27.5 - - - +
415D ASN 3.1 8.7 + - - +
416D VAL 3.6 7.6 - - - +
418D THR* 1.3 75.8 - - - +
420D ALA* 1.3 65.7 + - - +
422D GLY* 3.2 2.1 + - - -
423D ILE* 3.0 31.4 + - + +
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Residues in contact with ALA 420 (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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382D LEU* 4.9 1.3 - - + +
405D LEU* 3.7 33.3 - - + +
408D LEU* 4.3 13.2 - - + -
409D LEU* 3.8 8.1 - - + -
416D VAL 3.0 13.2 + - - +
417D VAL* 3.3 9.4 + - - +
419D CYS* 1.3 75.6 - - - +
421D ALA* 1.3 57.3 + - - +
423D ILE* 3.6 9.9 + - - +
424D LEU* 3.0 36.0 + - - +
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Residues in contact with ALA 421 (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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409D LEU* 3.9 12.1 - - + +
417D VAL 2.9 17.0 + - - +
418D THR* 3.5 8.1 - - - +
419D CYS 3.2 0.2 - - - -
420D ALA* 1.3 77.6 - - - +
422D GLY* 1.3 57.5 + - - +
424D LEU* 3.5 6.2 + - - +
425D SER* 2.9 29.3 + - - -
447D LEU* 4.9 3.1 - - + -
450D THR* 5.0 4.7 - - + -
460D ILE 4.7 2.2 - - - +
463D PRO* 3.9 11.1 - - + +
464D ALA* 4.2 27.8 - - + +
467D ALA* 4.5 1.4 - - - +
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Residues in contact with GLY 422 (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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386D ARG* 4.5 3.8 - - - -
418D THR 3.2 10.4 + - - -
419D CYS 3.7 2.0 - - - -
421D ALA* 1.3 75.8 - - - +
423D ILE* 1.3 66.3 + - - +
425D SER* 3.3 3.6 + - - -
426D ASN* 3.1 27.0 + - - +
463D PRO* 3.6 18.3 - - - +
21E PHE* 4.0 22.1 - - - -
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Residues in contact with ILE 423 (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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363D MET* 5.0 2.2 - - + -
382D LEU* 3.7 37.0 - - + +
385D LEU* 3.9 16.6 - - + +
386D ARG* 3.5 24.0 - - + +
389D SER* 4.1 11.4 - - - -
401D LEU* 5.5 1.3 - - + -
405D LEU* 3.5 29.8 - - + -
419D CYS 3.0 27.6 + - - +
420D ALA 3.8 2.7 - - - +
422D GLY* 1.3 75.7 - - - +
424D LEU* 1.3 63.7 + - - +
426D ASN* 3.1 4.5 + - - +
427D LEU* 2.9 37.4 + - + +
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Residues in contact with LEU 424 (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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402D LEU* 4.1 15.3 - - + +
405D LEU* 4.0 29.8 - - + -
406D VAL* 4.2 10.5 - - + +
409D LEU* 3.9 29.2 - - + -
420D ALA 3.0 23.3 + - - +
421D ALA* 3.7 5.4 - - - +
423D ILE* 1.3 77.3 - - - +
425D SER* 1.3 60.8 + - - +
427D LEU* 3.8 3.9 - - - -
428D THR* 2.8 34.4 + - + +
438D VAL* 3.8 31.9 - - + -
447D LEU* 4.8 8.5 - - + -
467D ALA* 4.5 8.5 - - + -
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Residues in contact with SER 425 (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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421D ALA 2.9 20.0 + - - -
422D GLY* 3.4 9.2 - - - -
424D LEU* 1.3 76.7 - - - +
426D ASN* 1.3 61.8 + - - +
428D THR* 3.1 2.6 + - - -
463D PRO* 3.3 14.3 + - - -
466D CYS* 3.2 29.8 - - - +
467D ALA* 3.5 13.7 + - - +
470D HIS* 2.8 33.8 + - - -
17E GLU 5.2 0.9 + - - -
19E ILE* 4.1 10.1 - - - +
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Residues in contact with ASN 426 (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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386D ARG 4.4 0.4 + - - -
389D SER* 2.9 41.0 + - - +
390D ASP* 3.7 14.5 - - - +
393D THR* 3.3 15.0 - - - +
422D GLY 3.1 4.1 + - - +
423D ILE 3.1 3.5 + - - +
425D SER* 1.3 78.5 + - - +
427D LEU* 1.3 64.8 + - - +
429D CYS* 3.2 20.0 - - - +
17E GLU 4.5 0.7 - - - +
18E LEU* 3.5 10.8 - - - +
19E ILE* 3.1 45.9 + - - +
21E PHE* 3.6 13.6 - - - -
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Residues in contact with LEU 427 (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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363D MET* 4.0 6.7 - - + -
389D SER* 4.3 7.9 - - - +
392D ALA* 3.7 27.4 - - + +
393D THR* 4.8 5.6 - - - +
398D MET* 3.7 30.7 - - + -
401D LEU* 4.3 7.2 - - + -
402D LEU* 3.9 30.1 - - + -
405D LEU* 4.3 6.5 - - + -
423D ILE* 2.9 41.5 + - + +
424D LEU 4.0 3.1 - - - +
426D ASN* 1.3 76.9 - - - +
428D THR* 1.3 59.1 + - - +
429D CYS 3.3 0.9 - - - +
431D ASN* 3.6 11.3 - - - +
434D ASN* 3.2 20.1 - - - +
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Residues in contact with THR 428 (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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402D LEU* 5.6 0.4 - - + -
424D LEU* 2.8 26.7 + - + +
425D SER* 3.1 11.1 + - - -
427D LEU* 1.3 76.8 - - + +
429D CYS* 1.3 62.1 + - - +
430D ASN 3.0 0.3 + - - -
431D ASN 3.5 4.2 + - - -
434D ASN* 4.4 9.4 - - + +
435D LYS* 3.0 39.4 - - - +
438D VAL* 4.1 21.5 - - + -
467D ALA* 4.2 5.5 - - + -
470D HIS* 3.2 21.5 - - - +
471D LEU* 4.0 24.2 - - + -
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Residues in contact with CYS 429 (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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393D THR* 3.9 18.9 + - - -
425D SER 3.9 2.0 - - - +
426D ASN 3.2 16.1 + - - +
427D LEU 3.3 1.0 - - - -
428D THR* 1.3 74.0 - - - +
430D ASN* 1.3 74.5 + - - +
431D ASN* 3.2 1.9 + - - +
470D HIS* 3.2 21.6 - - - +
16E ASP* 3.8 10.3 - - - -
17E GLU* 3.6 35.2 - - - +
18E LEU* 3.6 24.5 - - + -
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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