Contacts of the helix formed by residues 413 - 425 (chain D) in PDB entry 2W3S
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 VAL 413 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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379D PRO* 5.8 1.6 - - - -
380D PRO* 4.8 9.9 - - + -
411D ASP* 3.3 17.9 - - - +
412D CYS* 1.3 75.2 - - - +
414D LEU* 1.3 65.3 + - - +
415D GLY 3.2 3.4 + - - -
416D GLU* 3.4 8.3 + - + +
417D LEU* 3.2 25.6 + - + +
624D TYR* 4.1 24.1 - - + -
650D ASP* 4.7 4.9 - - - +
713D TRP* 3.9 30.0 - - + +
715D GLN* 3.6 23.6 - - - +
726D LYS* 5.4 2.2 - - - +
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Residues in contact with LEU 414 (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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318D SER* 3.4 36.1 - - - +
376D PHE* 3.8 20.9 - - + -
412D CYS* 3.5 14.5 - - - -
413D VAL* 1.3 75.0 - - - +
415D GLY* 1.3 58.8 + - - +
417D LEU* 4.4 6.1 - - + -
418D VAL* 2.7 50.5 + - + +
452D PRO* 3.7 15.0 - - + -
453D VAL 3.9 6.1 - - - +
454D LYS* 4.5 0.7 - - + -
624D TYR* 3.6 25.8 - - + -
625D GLY 3.7 30.1 - - - +
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Residues in contact with GLY 415 (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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376D PHE* 3.8 17.4 - - - +
377D TYR 5.7 1.0 + - - -
379D PRO* 6.3 5.3 - - - +
412D CYS* 5.3 1.4 + - - -
413D VAL 3.2 1.2 + - - -
414D LEU* 1.3 83.6 - - - +
416D GLU* 1.3 62.4 + - - +
418D VAL* 4.0 1.9 - - - +
419D THR* 3.2 23.1 + - - -
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Residues in contact with GLU 416 (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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413D VAL* 3.4 6.6 + - - +
415D GLY* 1.3 71.4 - - - +
417D LEU* 1.3 57.8 + - - +
419D THR* 3.2 8.9 + - - -
420D ARG* 2.9 46.0 + - - +
713D TRP* 3.7 26.8 - - + -
715D GLN* 5.0 4.3 + - - -
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Residues in contact with LEU 417 (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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413D VAL* 3.2 22.1 + - + +
414D LEU* 3.8 4.3 - - + +
416D GLU* 1.3 79.1 - - - +
418D VAL* 1.3 62.2 + - + +
420D ARG* 3.0 4.7 + - - +
421D LEU* 2.8 26.7 + - - +
624D TYR* 5.1 0.7 - - + -
625D GLY* 4.1 13.5 - - - +
626D ALA* 3.5 34.1 - - + +
648D LEU* 3.6 34.6 - - + +
650D ASP* 4.5 7.0 - - + +
713D TRP* 3.5 51.0 - - + -
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Residues in contact with VAL 418 (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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369D ALA 5.8 0.9 - - - +
373D ALA* 5.7 5.6 - - + -
376D PHE* 3.8 29.8 - - + -
414D LEU* 2.7 41.2 + - + +
415D GLY 4.0 2.0 - - - +
417D LEU* 1.3 73.8 - - + +
419D THR* 1.3 56.9 - - - +
421D LEU* 3.4 5.3 + - - +
422D GLN* 3.0 40.6 + - - +
450D LEU* 3.6 27.8 - - + -
452D PRO* 4.9 2.5 - - + -
626D ALA* 4.0 16.4 - - + -
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Residues in contact with THR 419 (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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415D GLY 3.2 13.0 + - - -
416D GLU* 3.2 11.1 + - - -
417D LEU 3.2 0.4 - - - -
418D VAL* 1.3 74.6 - - - +
420D ARG* 1.3 64.8 + - - +
422D GLN* 3.6 9.3 + - - +
423D LYS* 3.1 54.5 + - + +
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Residues in contact with ARG 420 (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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416D GLU* 2.9 39.5 + - - +
417D LEU* 3.0 8.7 + - - +
419D THR* 1.3 77.8 - - - +
421D LEU* 1.3 58.7 + - - +
423D LYS* 3.9 4.3 - - - +
424D SER* 2.8 35.5 + - - +
648D LEU* 3.9 15.7 - - + -
713D TRP* 3.7 27.1 - - - -
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Residues in contact with LEU 421 (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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417D LEU 2.8 15.6 + - - +
418D VAL* 3.8 5.2 - - - +
420D ARG* 1.3 76.0 - - - +
422D GLN* 1.3 56.5 + - - +
424D SER* 3.2 8.3 + - - +
425D ALA* 2.7 39.5 + - + +
450D LEU* 4.4 4.0 - - + -
626D ALA* 3.5 42.4 - - + +
627D ALA 3.8 3.4 - - - +
628D ILE* 3.8 19.7 - - + -
646D ASP* 3.7 37.0 - - + +
647D ILE 4.2 1.3 - - - -
648D LEU* 3.9 23.3 - - + +
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Residues in contact with GLN 422 (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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369D ALA* 3.7 18.0 + - - +
373D ALA* 6.2 0.6 - - - +
418D VAL* 3.0 31.5 + - - +
419D THR* 4.2 7.7 + - - +
421D LEU* 1.3 75.0 - - - +
423D LYS* 1.3 59.6 + - + +
425D ALA 3.6 0.2 - - - -
426D ASN 3.0 7.1 + - - -
427D PHE* 2.8 76.3 + - + +
428D THR* 5.8 1.1 - - - +
450D LEU* 3.6 26.2 - - + +
628D ILE* 3.9 4.0 - - + -
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Residues in contact with LYS 423 (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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419D THR* 3.1 43.1 + - + +
420D ARG* 3.9 3.8 - - - +
421D LEU 3.2 0.6 - - - -
422D GLN* 1.3 76.0 - - + +
424D SER* 1.3 66.6 + - - +
426D ASN* 3.1 14.3 + - - +
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Residues in contact with SER 424 (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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420D ARG* 2.8 27.7 + - - +
421D LEU* 3.2 15.9 + - - +
423D LYS* 1.3 78.1 - - - +
425D ALA* 1.3 58.9 + - - +
426D ASN* 3.3 2.9 + - - +
644D ARG* 4.8 3.3 + - - -
648D LEU* 5.9 0.3 - - - +
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Residues in contact with ALA 425 (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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421D LEU* 2.7 24.4 + - + +
422D GLN 4.0 0.9 - - - +
424D SER* 1.3 71.4 + - - +
426D ASN* 1.3 59.2 + - - +
427D PHE* 4.6 0.9 - - + +
430D ARG* 2.8 38.6 + - - +
628D ILE* 3.8 19.1 - - + -
644D ARG* 3.7 12.2 + - - +
646D ASP* 3.8 27.4 - - + -
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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