Contacts of the helix formed by residues 435 - 443 (chain B) in PDB entry 4LQL
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 435 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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405B TYR* 4.8 6.7 - - - +
428B PRO* 5.1 5.6 - - - -
430B ILE* 3.6 17.7 - - - -
431B GLY 2.8 12.2 + - - -
433B ALA 3.6 0.2 - - - -
434B GLU* 1.3 80.8 - - - +
436B ALA* 1.3 59.5 + - - +
437B LYS 3.1 2.2 - - - +
438B GLN 4.0 2.0 - - - -
439B TRP* 3.2 25.5 + - - +
473B ILE* 4.3 12.8 - - - +
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Residues in contact with ALA 436 (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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431B GLY 3.6 4.2 + - - -
432B LEU* 4.1 29.4 - - + +
434B GLU 4.5 0.4 - - - +
435B GLY* 1.3 76.1 - - - +
437B LYS* 1.3 59.9 + - + +
439B TRP* 3.9 2.6 - - - +
440B MET* 2.9 35.9 + - + +
131C ARG* 3.5 30.5 + - - +
148C TYR* 4.8 8.1 - - + -
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Residues in contact with LYS 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B ALA* 3.2 35.4 - - - +
434B GLU 5.1 1.1 - - - -
435B GLY 3.1 1.7 - - - +
436B ALA* 1.3 78.8 - - - +
438B GLN* 1.3 59.8 + - - +
439B TRP 3.3 1.3 - - - -
440B MET* 3.6 7.5 - - - +
441B LYS* 3.0 28.5 + - - +
146C SER* 3.7 25.2 + - - +
147C VAL* 5.4 0.2 - - - -
148C TYR* 3.7 31.2 - - + +
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Residues in contact with GLN 438 (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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434B GLU 4.5 8.8 + - - +
435B GLY* 4.0 3.0 + - - +
437B LYS* 1.3 77.5 - - - +
439B TRP* 1.3 58.2 + - - +
441B LYS* 3.2 12.7 - - + +
442B TYR* 3.2 27.2 + - - +
473B ILE* 3.7 33.7 - - + +
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Residues in contact with TRP 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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390B ASP* 3.2 37.5 - - - -
392B THR* 4.1 10.1 - - - -
403B ILE* 3.6 19.3 - - + -
404B GLY* 4.5 1.8 - - - -
405B TYR* 3.2 36.3 - + + -
435B GLY 3.2 19.2 + - - +
436B ALA* 4.1 4.7 - - - +
437B LYS 3.3 0.2 - - - -
438B GLN* 1.3 77.8 - - - +
440B MET* 1.3 64.1 + - - +
442B TYR* 3.6 2.3 + - - +
443B GLY 2.7 34.6 + - - +
444B GLY 2.4 27.7 + - - -
445B GLY 3.3 10.2 + - - -
448B THR* 3.6 31.2 - - + -
473B ILE* 3.6 12.0 - - + +
131C ARG* 3.8 27.5 - - + +
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Residues in contact with MET 440 (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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436B ALA* 2.9 25.9 + - + +
437B LYS* 3.6 9.6 - - - +
439B TRP* 1.3 76.7 - - - +
441B LYS* 1.3 65.4 + - - +
443B GLY 3.8 4.2 + - - -
102C HIS* 5.7 5.8 - - + -
104C ALA* 5.4 2.7 - - + -
130C ASP* 5.1 7.9 - - + -
131C ARG* 4.9 18.6 - - + +
134C ALA* 3.4 41.6 - - + +
138C SER* 4.4 0.5 - - - -
146C SER* 4.7 11.7 - - - +
148C TYR* 5.2 8.1 - - + -
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Residues in contact with LYS 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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437B LYS 3.0 27.5 + - - +
438B GLN* 3.2 15.9 - - + +
440B MET* 1.3 74.9 - - - +
442B TYR* 1.3 60.4 + - + +
443B GLY 3.2 0.4 - - - -
138C SER* 3.0 25.6 - - - -
146C SER* 6.0 2.9 - - - -
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Residues in contact with TYR 442 (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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396B PHE* 5.2 8.7 - - - -
401B LYS* 5.8 2.6 - - - +
403B ILE* 4.2 14.9 - - + +
438B GLN 3.2 13.4 + - - +
439B TRP* 3.6 3.1 + - - +
440B MET 3.5 0.2 - - - -
441B LYS* 1.3 77.7 - - + +
443B GLY* 1.3 59.5 + - - +
471B ILE* 4.3 26.7 - - + -
473B ILE* 5.4 2.0 - - + -
138C SER* 4.4 3.9 - - - -
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Residues in contact with GLY 443 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B PHE* 5.9 4.3 - - - -
403B ILE* 4.4 6.4 - - - +
439B TRP* 2.7 28.4 + - - +
440B MET 3.8 3.5 + - - -
441B LYS 3.2 5.7 + - - -
442B TYR* 1.3 80.7 - - - +
444B GLY* 1.3 66.9 + - - +
131C ARG 5.4 0.9 - - - -
134C ALA* 4.6 6.5 - - - -
135C TYR* 4.6 7.9 - - - -
138C SER* 4.2 12.3 - - - -
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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