Contacts of the helix formed by residues 429 - 441 (chain B) in PDB entry 3H44
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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427B LYS 4.0 0.4 + - - -
428B GLU* 1.3 75.7 - - - +
430B PRO* 1.4 72.4 - - + +
431B ARG* 4.9 3.8 - - + +
432B GLY* 3.5 7.2 + - - +
433B TYR* 3.1 19.5 + - - +
898B LYS* 3.6 33.0 - - + +
899B LYS* 3.6 35.7 - - - +
902B ALA* 4.4 13.5 - - - +
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Residues in contact with PRO 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B THR* 3.8 9.9 - - - +
85B LYS* 3.7 31.0 - - + +
87B SER* 3.3 18.4 + - - +
152B ASP* 5.2 2.0 - - + +
259B LEU* 3.9 25.1 - - + -
428B GLU 3.8 3.6 - - - +
429B ARG* 1.4 91.1 - - + +
431B ARG* 1.3 65.9 + - - +
433B TYR* 2.9 17.9 + - + +
434B THR* 2.9 15.8 + - - +
898B LYS* 4.0 15.3 - - + -
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Residues in contact with ARG 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B SER* 3.5 10.6 + - - -
137B SER* 3.1 30.2 + - - -
138B SER 4.4 2.8 + - - +
139B ASN* 4.2 15.4 - - - +
150B TYR* 3.6 39.5 + - + +
151B PHE 4.2 7.9 - - - -
152B ASP* 3.5 36.4 + - - +
429B ARG* 3.5 3.0 - - + +
430B PRO* 1.3 77.3 - - - +
432B GLY* 1.3 65.1 + - - +
434B THR* 3.1 13.8 + - - -
435B SER* 3.4 13.9 + - - -
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Residues in contact with GLY 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428B GLU* 5.7 0.2 - - - -
429B ARG* 3.5 9.4 + - - +
430B PRO 3.3 0.6 - - - -
431B ARG* 1.3 78.2 - - - +
433B TYR* 1.3 58.7 + - - +
435B SER* 3.6 3.3 + - - -
436B LYS* 3.0 33.5 + - - +
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Residues in contact with TYR 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B ASP* 4.6 0.7 + - - -
62B ARG* 3.6 25.5 + - - -
64B TYR* 3.0 31.6 + + - -
78B ILE* 4.1 22.4 - - + -
259B LEU* 4.3 6.5 - - + -
425B LYS* 4.8 7.0 + - - -
428B GLU* 3.5 39.5 + - + +
429B ARG 3.1 17.9 + - - +
430B PRO* 2.9 9.9 + - + +
432B GLY* 1.3 69.5 - - - +
434B THR* 1.3 62.3 + - - +
436B LYS* 3.7 7.1 - - + +
437B ILE* 2.8 54.2 + - + +
450B LEU* 3.3 24.2 - - + +
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Residues in contact with THR 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ILE* 4.7 0.4 - - + -
87B SER* 2.8 43.0 + - - +
88B ALA 3.8 7.4 + - - -
89B ALA* 3.6 17.1 - - - +
150B TYR* 4.8 0.7 - - - +
257B VAL* 3.7 28.6 - - + +
259B LEU* 3.9 19.1 - - + -
430B PRO 2.9 6.9 + - - +
431B ARG* 3.1 9.0 + - - -
433B TYR* 1.3 75.8 - - - +
435B SER* 1.3 58.4 + - - +
438B ALA* 2.9 32.4 + - - +
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Residues in contact with SER 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ALA* 3.5 10.7 - - - +
141B PHE* 4.0 7.1 - - - -
148B ASN* 2.7 43.6 + - - +
150B TYR* 3.5 21.6 - - - -
431B ARG 3.4 15.1 + - - -
432B GLY* 3.9 4.5 - - - -
433B TYR 3.3 0.4 - - - -
434B THR* 1.3 81.3 + - - +
436B LYS* 1.3 62.8 + - - +
438B ALA* 3.4 0.7 + - - +
439B GLY* 3.2 12.3 + - - -
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Residues in contact with LYS 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B GLY 3.0 20.4 + - - +
433B TYR* 3.7 8.3 - - + +
435B SER* 1.3 74.5 + - - +
437B ILE* 1.3 69.3 + - + +
439B GLY* 3.1 12.3 + - - -
440B ILE* 3.3 40.6 + - + +
453B GLU* 3.4 22.2 + - - -
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Residues in contact with ILE 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B LEU* 3.7 24.9 - - + -
78B ILE* 5.1 0.2 - - + -
257B VAL* 3.6 25.6 - - + -
433B TYR* 2.8 63.6 + - + +
434B THR* 3.8 0.7 - - - +
436B LYS* 1.3 71.2 - - + +
438B ALA* 1.3 56.5 + - - +
439B GLY 2.9 4.5 - - - -
440B ILE* 2.8 38.5 + - + +
441B LEU* 3.0 17.6 + - + +
449B VAL* 4.6 10.5 - - + +
450B LEU* 3.9 17.5 - - + -
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Residues in contact with ALA 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ALA* 4.2 15.0 - - + +
91B ASP* 3.3 30.2 - - + +
148B ASN* 4.6 0.2 - - - +
255B ALA* 3.5 28.2 - - - +
257B VAL* 3.4 16.3 - - + +
434B THR 2.9 17.9 + - - +
435B SER 3.4 5.4 + - - +
437B ILE* 1.3 76.1 - - - +
439B GLY* 1.3 58.9 + - - +
440B ILE 3.7 0.2 + - - -
441B LEU* 3.8 6.1 - - - +
442B HIS* 3.7 3.1 - - - -
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Residues in contact with GLY 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B ASP* 3.9 17.9 - - - +
146B HIS* 4.0 3.6 - - - -
148B ASN* 4.5 0.9 - - - -
435B SER 3.2 8.9 + - - -
436B LYS* 3.1 9.3 + - - -
437B ILE 2.9 1.8 + - - -
438B ALA* 1.3 79.6 - - - +
440B ILE* 1.3 62.4 + - - +
441B LEU 3.7 0.2 + - - -
442B HIS* 3.7 8.3 - - - -
443B TYR* 3.3 23.2 - - - -
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Residues in contact with ILE 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B LYS* 3.3 32.1 + - + +
437B ILE* 2.8 30.8 + - + +
439B GLY* 1.3 73.6 - - - +
441B LEU* 1.3 60.3 + - - +
442B HIS 3.0 2.0 - - - -
443B TYR* 2.9 30.9 + - + +
444B TYR* 3.4 24.8 + - + +
449B VAL* 4.1 27.9 - - + +
453B GLU* 3.5 42.8 - - + +
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Residues in contact with LEU 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B LYS* 4.1 21.3 - - + +
75B VAL 4.2 6.7 - - - +
76B LEU* 4.0 13.0 - - + +
255B ALA* 3.6 27.6 - - + -
256B VAL 3.7 12.8 - - - +
257B VAL* 3.5 31.9 - - + -
437B ILE* 3.0 13.2 + - + +
438B ALA* 3.8 2.2 - - - +
439B GLY 3.4 0.4 - - - -
440B ILE* 1.3 76.2 - - - +
442B HIS* 1.3 57.2 + - - +
443B TYR 3.2 3.4 + - - -
444B TYR 3.7 11.1 + - - +
446B LEU* 3.9 28.7 - - + +
449B VAL* 3.6 27.8 - - + -
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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