Contacts of the helix formed by residues 428 - 439 (chain A) in PDB entry 1LAN
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 428 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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336A ARG* 4.8 2.4 + - - -
361A THR* 4.0 6.1 - - - +
363A ALA* 3.7 19.9 - - - +
425A ARG 4.1 7.3 + - - -
426A SER 3.4 4.3 + - - -
427A ALA* 1.3 74.5 - - - +
429A ALA* 1.3 62.7 + - - +
431A THR* 3.1 18.9 + - - -
432A ALA* 3.1 14.7 + - - +
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Residues in contact with ALA 429 (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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361A THR* 3.4 24.0 - - - +
363A ALA* 3.5 8.7 - - + +
364A MET* 4.1 22.9 - - - +
376A PHE* 3.4 23.1 - - + -
400A MET* 5.0 6.1 - - + -
427A ALA 3.3 0.6 - - - -
428A GLY* 1.3 76.4 - - - +
430A CYS* 1.3 57.3 + - - +
432A ALA* 3.5 2.4 + - - +
433A ALA* 3.1 22.7 + - - +
447A HIS* 5.2 1.0 + - - -
449A ASP* 4.0 9.5 - - - +
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Residues in contact with CYS 430 (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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376A PHE* 3.7 26.4 - - + -
400A MET* 4.5 11.0 - - - -
401A PRO* 3.9 24.6 - - - +
402A LEU* 5.4 0.7 - - - +
406A TYR* 3.6 39.7 - - + +
427A ALA* 2.9 15.0 + - - +
429A ALA* 1.3 75.5 - - - +
431A THR* 1.3 59.1 + - - +
433A ALA* 3.4 3.3 + - - +
434A ALA* 2.9 26.9 + - - +
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Residues in contact with THR 431 (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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336A ARG* 4.4 4.2 + - - -
406A TYR* 4.0 23.3 - - + +
409A GLN* 3.9 29.4 - - + +
410A VAL* 3.6 16.2 - - - +
422A GLY* 4.7 13.7 + - - -
424A TYR 5.6 1.8 + - - +
426A SER 4.4 5.9 + - - +
427A ALA 3.0 14.4 + - - +
428A GLY* 3.1 17.7 + - - -
430A CYS* 1.3 72.7 - - - +
432A ALA* 1.3 60.5 + - - +
434A ALA* 3.5 8.1 - - - +
435A PHE* 2.9 27.9 + - - +
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Residues in contact with ALA 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A ARG* 3.5 34.7 - - - +
360A LEU* 3.8 15.9 - - + +
361A THR* 3.7 16.2 - - + -
428A GLY 3.1 17.9 + - - +
429A ALA 3.7 3.1 - - - +
430A CYS 3.3 0.2 - - - -
431A THR* 1.3 75.8 + - - +
433A ALA* 1.3 63.3 + - - +
435A PHE* 3.1 6.6 + - - +
436A LEU* 3.1 26.4 + - - +
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Residues in contact with ALA 433 (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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376A PHE* 3.5 37.7 - - + -
402A LEU* 4.1 6.5 - - + +
429A ALA 3.1 18.2 + - - +
430A CYS 3.6 3.8 - - - +
431A THR 3.3 0.2 - - - -
432A ALA* 1.3 75.1 - - - +
434A ALA* 1.3 63.9 + - - +
436A LEU* 3.2 7.1 + - - +
437A LYS* 3.1 21.5 + - - +
445A TRP* 3.8 5.9 - - + -
447A HIS* 3.8 19.6 - - + -
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Residues in contact with ALA 434 (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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402A LEU* 4.5 6.6 - - + +
403A PHE 5.0 1.6 - - - +
406A TYR* 3.7 9.0 - - + +
407A THR* 3.6 39.2 + - - +
410A VAL* 4.5 3.8 - - + -
430A CYS 2.9 17.8 + - - +
431A THR 3.3 6.0 + - - +
433A ALA* 1.3 74.1 - - - +
435A PHE* 1.3 63.5 + - - +
437A LYS* 3.1 23.0 + - - +
438A GLU* 3.5 12.3 + - - +
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Residues in contact with PHE 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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326A ILE* 3.7 35.7 - - + -
336A ARG* 3.4 56.5 - - + +
337A LEU* 4.4 2.7 - - + -
340A ALA* 4.4 0.9 - - + -
410A VAL* 4.2 12.5 - - + +
418A VAL* 3.6 20.2 - - + -
419A ASN 3.3 26.7 - - - -
420A ASN* 3.8 5.6 - - - -
431A THR 2.9 13.1 + - - +
432A ALA 3.2 10.3 - - - +
434A ALA* 1.3 76.0 - - - +
436A LEU* 1.3 65.5 + - - +
438A GLU* 3.2 20.3 + - - +
439A PHE* 3.4 27.8 - + - -
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Residues in contact with LEU 436 (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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336A ARG* 4.0 24.7 - - + +
339A LEU* 3.7 35.9 - - + -
340A ALA* 4.7 1.3 - - - +
343A LEU* 4.1 10.5 - - + +
356A ASN* 4.2 7.2 - - - +
360A LEU* 4.1 9.9 - - + -
432A ALA 3.1 15.8 + - - +
433A ALA 3.2 6.2 + - - +
435A PHE* 1.3 77.5 - - + +
437A LYS* 1.3 56.1 + - - +
439A PHE* 2.9 27.6 + - - +
440A VAL* 3.6 8.3 - - - +
445A TRP* 3.9 13.2 - - + -
447A HIS* 3.6 44.0 - - + +
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Residues in contact with LYS 437 (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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378A ASN* 6.0 4.5 - - + +
402A LEU* 3.8 42.4 + - + +
403A PHE 4.5 6.8 - - - -
404A GLU* 4.6 4.0 - - - +
407A THR* 3.9 20.1 + - - -
433A ALA 3.1 11.2 + - - +
434A ALA* 3.1 11.6 + - - +
436A LEU* 1.3 71.2 - - - +
438A GLU* 1.3 63.2 + - - +
439A PHE 3.0 10.3 + - - -
440A VAL* 3.1 27.4 + - + +
445A TRP* 3.7 27.1 - - + -
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Residues in contact with GLU 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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322A ASN* 4.2 2.8 + - - -
324A LYS* 3.0 42.9 + - + +
407A THR* 3.4 29.2 + - + +
410A VAL* 5.0 1.1 - - + -
411A ILE* 4.2 19.8 - - + +
418A VAL* 4.6 10.5 - - + -
434A ALA 3.7 13.9 - - - +
435A PHE* 3.4 14.4 - - - +
436A LEU 3.1 1.0 - - - -
437A LYS* 1.3 81.5 - - - +
439A PHE* 1.3 69.9 + - + +
440A VAL 3.5 0.7 - - - -
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Residues in contact with PHE 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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320A ALA* 3.6 25.6 - - + -
322A ASN* 3.6 28.5 - - - +
324A LYS* 4.0 11.7 - - + -
326A ILE* 3.8 25.1 - - + -
340A ALA* 3.7 37.2 - - + +
343A LEU* 4.0 13.3 - - + +
344A CYS* 4.2 5.8 + - + +
347A HIS* 3.5 14.2 - - - -
418A VAL* 4.2 10.3 - - + -
435A PHE* 3.4 43.3 - + - -
436A LEU* 2.9 10.0 + - - +
438A GLU* 1.3 82.7 - - + +
440A VAL* 1.3 63.3 - - - +
441A THR* 5.7 1.3 - - - -
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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