Contacts of the helix formed by residues 425 - 435 (chain D) in PDB entry 2G4C
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 LEU 425 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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386D ASP* 6.2 0.2 - - - +
389D ARG* 6.0 4.5 - - - +
424D SER* 1.3 79.8 + - - +
426D GLU* 1.3 65.6 + - - +
427D GLN 3.4 0.4 - - - -
428D LEU* 3.3 5.9 + - + +
429D TYR* 2.6 88.0 + - + +
442D LEU* 4.0 20.9 - - + -
463D LYS* 4.9 6.5 - - - +
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Residues in contact with GLU 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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424D SER* 3.0 7.0 + - - +
425D LEU* 1.3 98.8 - - - +
427D GLN* 1.3 68.0 + - + +
428D LEU 3.0 1.8 - - - -
429D TYR* 3.8 11.2 - - + +
430D SER* 3.0 29.6 + - - -
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Residues in contact with GLN 427 (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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423D SER* 2.9 29.4 - - - +
424D SER* 3.3 11.2 + - - +
425D LEU 3.4 0.2 - - - -
426D GLU* 1.3 81.0 - - - +
428D LEU* 1.3 59.7 + - + +
430D SER* 3.7 5.4 + - - -
431D LYS* 3.0 40.8 + - - +
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Residues in contact with LEU 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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386D ASP* 4.1 14.8 - - - +
419D GLU* 3.9 23.1 - - - +
422D GLN 3.8 17.0 - - - +
423D SER* 4.0 9.9 - - - +
424D SER 3.6 22.7 - - - +
425D LEU* 3.3 7.9 + - + +
426D GLU 3.0 0.4 - - - -
427D GLN* 1.3 79.4 - - - +
429D TYR* 1.3 62.2 + - + +
430D SER 3.4 0.7 - - - -
431D LYS* 3.7 32.7 - - + +
432D TYR* 3.1 43.6 + - + +
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Residues in contact with TYR 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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425D LEU* 2.6 56.8 + - + +
426D GLU* 3.1 14.5 + - + +
428D LEU* 1.3 78.5 - - + +
430D SER* 1.3 54.3 + - - +
431D LYS 3.3 0.2 - - - -
432D TYR* 3.9 3.8 + + - +
433D ASP* 2.4 31.4 + - - +
440D THR* 4.2 21.7 + - + -
442D LEU* 3.1 26.2 - - + +
454D HIS 5.3 0.3 + - - -
455D LEU 5.5 0.2 - - - -
456D ARG* 3.2 64.1 + - + +
463D LYS* 3.8 21.6 - - - +
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Residues in contact with SER 430 (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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368D HIS 5.5 8.3 - - - -
370D LYS* 5.9 0.5 - - - +
426D GLU 3.0 17.2 + - - -
427D GLN* 3.7 7.3 + - - -
429D TYR* 1.3 76.5 - - - +
431D LYS* 1.3 65.1 + - - +
432D TYR 3.3 0.7 - - - -
433D ASP* 3.4 16.9 + - - +
434D GLU* 3.5 24.0 + - - +
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Residues in contact with LYS 431 (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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76D ARG* 3.0 52.8 + - - +
423D SER* 5.2 5.1 - - - -
427D GLN* 3.0 44.6 + - - +
428D LEU* 3.7 30.9 - - + +
429D TYR 3.3 0.2 - - - -
430D SER* 1.3 83.1 + - - +
432D TYR* 1.3 67.2 + - + +
433D ASP 3.6 0.2 + - - -
434D GLU* 3.6 6.4 + - - +
435D MET* 3.7 10.2 + - - +
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Residues in contact with TYR 432 (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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384D ALA* 3.7 5.8 - - + -
386D ASP* 3.3 24.8 + - - -
414D TRP* 3.4 33.6 - + - -
416D GLY* 4.0 0.3 - - - -
419D GLU* 3.3 23.5 + - - -
428D LEU* 3.1 30.5 + - + +
429D TYR* 3.9 5.8 + + - +
430D SER 3.3 0.6 - - - -
431D LYS* 1.3 82.7 - - + +
433D ASP* 1.3 63.5 + - - +
435D MET* 3.2 12.9 + - - +
436D SER 2.9 15.6 + - - -
437D ILE* 3.1 40.8 + - + +
440D THR* 3.1 38.1 - - + +
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Residues in contact with ASP 433 (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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371D VAL* 3.1 37.9 - - + +
372D LEU 3.2 15.2 + - - +
429D TYR 2.4 24.0 - - - +
430D SER* 3.4 15.5 + - - +
431D LYS 3.3 0.4 - - - -
432D TYR* 1.3 78.8 - - - +
434D GLU* 1.3 54.7 + - - +
436D SER* 2.7 25.1 + - - +
437D ILE 4.9 1.3 - - - +
456D ARG* 3.3 18.8 + - - -
457D SER 4.6 0.2 - - - +
458D ARG* 3.6 19.2 - - - +
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Residues in contact with GLU 434 (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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72D ILE* 3.1 42.9 - - + +
75D ARG* 3.3 21.3 + - - -
76D ARG* 3.3 46.0 + - + +
78D PHE* 3.6 4.0 - - - -
370D LYS* 4.5 16.4 - - + +
371D VAL* 4.8 0.4 - - - +
372D LEU* 2.9 36.5 - - - +
430D SER* 3.5 17.0 + - - +
431D LYS* 3.7 1.4 - - - +
432D TYR 3.2 0.2 - - - -
433D ASP* 1.3 71.3 - - - +
435D MET* 1.3 58.1 + - - +
436D SER 3.0 4.9 - - - -
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Residues in contact with MET 435 (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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199B LEU* 5.6 1.6 - - + -
76D ARG* 3.5 29.8 - - + +
78D PHE* 4.0 2.0 - - - -
102D LEU* 3.9 20.8 - - + +
380D PRO* 4.0 15.6 - - - +
381D ILE* 3.7 17.5 + - + +
414D TRP* 3.7 45.1 - - + -
431D LYS* 3.7 9.2 - - - +
432D TYR* 3.2 30.1 + - - +
434D GLU* 1.3 74.1 - - - +
436D SER* 1.3 76.2 + - - +
437D ILE* 3.5 12.6 + - + +
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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