Contacts of the helix formed by residues 429 - 441 (chain A) in PDB entry 3N57
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 ARG 429 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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427A LYS 4.0 1.0 + - - +
428A GLU* 1.3 71.4 - - - +
430A PRO* 1.3 74.5 - - + +
431A ARG* 3.2 5.7 + - + +
432A GLY* 3.4 5.8 + - - +
433A TYR* 3.0 21.8 + - - +
898A LYS* 4.3 24.7 - - + +
899A LYS* 4.7 18.8 - - - +
902A ALA* 4.2 23.0 - - - +
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Residues in contact with PRO 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ARG* 6.2 0.2 - - - +
83A THR* 4.8 7.0 - - + -
85A LYS* 3.7 30.3 - - + +
87A SER* 3.2 11.0 + - - +
152A ASP* 5.4 2.7 - - + +
259A LEU* 3.8 34.5 - - + -
428A GLU 3.6 5.8 - - - +
429A ARG* 1.3 84.5 - - + -
431A ARG* 1.3 58.7 + - + +
433A TYR* 3.3 6.7 + - + +
434A THR* 2.9 34.0 + - - +
898A LYS* 4.0 21.1 - - + -
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Residues in contact with ARG 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A SER* 3.6 9.8 - - - -
137A SER* 3.5 27.2 + - - -
138A SER* 5.1 1.8 + - - +
139A ASN* 4.3 11.7 + - - +
150A TYR* 3.6 41.7 + - + +
151A PHE 4.3 7.0 - - - -
152A ASP* 3.3 37.7 + - + +
429A ARG* 3.2 4.1 + - + +
430A PRO* 1.3 80.4 - - - +
432A GLY* 1.3 60.6 + - - +
434A THR* 2.9 16.3 + - - -
435A SER* 3.2 12.3 + - - -
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Residues in contact with GLY 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A TYR* 6.2 0.2 - - - -
429A ARG* 3.4 9.7 + - - +
431A ARG* 1.3 79.7 - - - +
433A TYR* 1.3 56.3 + - - +
435A SER* 3.7 5.6 - - - -
436A LYS* 3.0 32.4 + - - +
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Residues in contact with TYR 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ARG* 3.5 33.4 + - - -
64A TYR* 2.9 27.1 + + - -
78A ILE* 4.2 19.7 - - + -
259A LEU* 4.3 7.6 - - + -
425A LYS* 3.6 12.3 + - - -
428A GLU* 3.4 37.2 - - + +
429A ARG 3.0 19.0 + - - +
430A PRO* 3.5 4.7 - - + +
432A GLY* 1.3 75.6 - - - +
434A THR* 1.3 65.1 + - - +
436A LYS* 3.5 10.7 + - - +
437A ILE* 3.1 57.6 + - + +
450A LEU* 3.8 12.3 - - + +
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Residues in contact with THR 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ILE* 4.4 2.5 - - + -
87A SER* 2.7 31.4 + - - +
88A ALA 4.0 2.9 + - - -
89A ALA* 3.6 16.7 - - - +
150A TYR* 4.9 0.5 - - - +
151A PHE 4.9 0.2 + - - -
257A VAL* 3.7 40.9 - - + +
259A LEU* 3.9 22.2 - - + -
430A PRO 2.9 9.4 + - - +
431A ARG* 2.9 14.0 + - - -
433A TYR* 1.3 70.9 - - - +
435A SER* 1.3 60.9 + - - +
438A ALA* 2.8 31.9 + - - +
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Residues in contact with SER 435 (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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89A ALA* 3.5 11.0 - - - +
141A PHE* 4.3 6.2 - - - -
148A ASN* 2.7 34.6 + - - -
150A TYR* 3.4 23.9 - - - -
431A ARG 3.2 15.3 + - - -
432A GLY* 3.7 7.4 - - - -
434A THR* 1.3 83.7 + - - +
436A LYS* 1.3 63.6 + - - +
438A ALA* 3.4 0.9 + - - +
439A GLY* 3.3 14.4 + - - -
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Residues in contact with LYS 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A GLU* 6.4 1.1 - - - -
432A GLY 3.0 19.4 + - - +
433A TYR* 4.0 11.9 - - + +
434A THR 3.3 0.2 - - - -
435A SER* 1.3 77.5 - - - +
437A ILE* 1.3 61.7 + - + +
439A GLY* 3.0 17.2 + - - -
440A ILE* 3.3 23.1 + - + +
453A GLU* 5.0 11.4 + - - +
454A TYR* 6.0 4.6 - - - -
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Residues in contact with ILE 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A LEU* 3.8 22.9 - - + -
78A ILE* 4.6 3.6 - - + -
257A VAL* 3.6 17.5 - - + -
433A TYR* 3.1 59.4 + - + +
434A THR 3.9 2.2 - - - +
436A LYS* 1.3 74.5 - - + +
438A ALA* 1.3 68.0 + - - +
439A GLY 3.0 1.8 - - - -
440A ILE* 3.0 28.9 + - + +
441A LEU* 3.0 22.0 + - + +
449A VAL* 4.9 6.3 - - + +
450A LEU* 4.0 18.2 - - + -
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Residues in contact with ALA 438 (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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89A ALA* 4.0 17.0 - - + +
91A ASP* 3.2 35.5 - - + +
148A ASN* 4.2 1.1 - - - +
255A ALA* 3.4 20.4 - - - +
257A VAL* 3.4 16.4 - - + +
434A THR 2.8 18.8 + - - +
435A SER 3.4 6.7 - - - +
437A ILE* 1.3 76.2 - - - +
439A GLY* 1.3 60.1 - - - +
441A LEU* 4.0 5.3 + - - -
442A HIS* 3.7 1.9 - - - -
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Residues in contact with GLY 439 (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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91A ASP* 3.9 17.2 - - - +
146A HIS* 4.1 3.9 + - - -
148A ASN* 4.3 1.8 - - - -
435A SER 3.3 5.8 + - - -
436A LYS* 3.0 9.1 + - - -
437A ILE 3.0 1.2 - - - -
438A ALA* 1.3 81.1 - - - +
440A ILE* 1.3 62.1 + - - +
441A LEU 3.6 0.5 + - - -
442A HIS* 3.7 10.4 - - - -
443A TYR* 3.5 19.9 - - - -
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Residues in contact with ILE 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A LYS* 3.3 19.3 + - + +
437A ILE* 3.0 22.7 + - + +
439A GLY* 1.3 74.1 - - - +
441A LEU* 1.3 59.5 + - - +
442A HIS 2.9 6.1 - - - -
443A TYR* 2.8 25.7 + - + -
444A TYR* 3.2 34.0 + - + +
449A VAL* 2.8 44.0 - - + +
452A ALA* 4.8 1.8 - - + -
453A GLU* 3.7 35.9 - - + +
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Residues in contact with LEU 441 (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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74A LYS* 3.5 30.1 - - + +
75A VAL 4.6 1.1 - - - +
76A LEU* 4.1 16.6 - - + +
255A ALA* 3.7 27.8 - - + -
256A VAL 3.8 9.9 - - - +
257A VAL* 3.7 29.8 - - + -
437A ILE* 3.0 15.1 + - + +
439A GLY 3.4 0.6 - - - -
440A ILE* 1.3 77.3 - - - +
442A HIS* 1.3 58.8 + - - +
443A TYR 3.2 1.9 + - - -
444A TYR 3.5 11.5 - - - +
446A LEU* 3.9 29.2 - - + -
449A VAL* 3.8 27.1 - - + -
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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