Contacts of the helix formed by residues 430 - 445 (chain A) in PDB entry 6M17
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 SER 430 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A THR 5.4 0.7 - - - +
47A GLY* 2.9 32.9 + - - +
48A PHE* 3.9 3.8 + - - -
50A VAL* 4.6 2.8 + - - +
223A VAL* 5.6 3.8 - - - +
226A THR* 3.4 29.8 + - - -
227A SER* 5.5 1.3 - - - -
426A CYS 3.2 12.3 + - - -
427A LEU* 3.7 7.6 + - - +
429A LEU* 1.3 78.4 - - - +
431A SER* 1.3 60.2 + - - +
432A MET 3.3 0.2 - - - -
433A PHE* 3.6 28.9 - - - +
434A GLY 4.3 1.0 + - - -
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Residues in contact with SER 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLY 3.4 5.7 + - - -
48A PHE* 3.5 29.0 + - - +
50A VAL 2.8 27.7 + - - -
51A GLY 4.0 0.2 + - - -
129A TYR* 3.4 25.0 + - - -
427A LEU 3.1 9.7 + - - -
428A GLY 4.5 0.2 - - - -
429A LEU 3.2 1.0 - - - -
430A SER* 1.3 74.9 + - - +
432A MET* 1.3 60.1 + - - +
433A PHE 3.3 0.9 - - - -
435A ASN* 3.5 16.8 - - - +
705A LEU* 3.9 12.8 + - - +
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Residues in contact with MET 432 (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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126A GLY* 3.8 25.4 - - - +
129A TYR* 3.6 26.5 - - + -
130A ASN* 3.8 12.8 - - + +
133A ILE* 4.0 10.3 - - + -
205A TRP* 4.3 4.7 - - + -
208A LEU* 3.7 40.9 - - + +
428A GLY 3.6 14.8 - - - +
429A LEU* 3.1 12.7 + - + +
431A SER* 1.3 74.9 - - - +
433A PHE* 1.3 65.8 + - - +
434A GLY 3.5 0.7 - - - -
435A ASN* 3.8 23.3 - - + +
436A MET* 3.3 26.1 + - - +
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Residues in contact with PHE 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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44A THR* 5.7 3.4 - - + -
208A LEU* 4.4 3.6 - - + -
211A CYS* 3.6 35.4 - - + -
212A THR* 3.6 20.7 - - + +
219A THR* 3.7 28.8 + - + +
222A ALA* 3.5 26.0 - - + -
223A VAL* 4.1 13.2 - - + -
226A THR* 4.5 6.5 - - + -
289A PHE* 4.6 4.4 - - + -
429A LEU* 3.4 35.4 + - + -
430A SER* 3.6 24.7 - - - +
431A SER 3.3 1.2 - - - -
432A MET* 1.3 78.8 - - - +
434A GLY* 1.3 60.9 + - - +
436A MET* 3.4 13.0 + - - +
437A GLU* 3.5 11.4 + - - +
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Residues in contact with GLY 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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44A THR* 6.0 0.2 - - - +
48A PHE* 3.4 29.5 - - - +
285A GLY* 4.2 5.9 - - - -
289A PHE* 3.6 29.7 - - - -
430A SER 4.3 1.2 + - - -
433A PHE* 1.3 77.5 - - - +
435A ASN* 1.3 61.7 + - - +
436A MET 3.2 0.2 - - - -
437A GLU* 3.2 12.6 + - - +
438A GLY* 3.3 9.0 + - - -
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Residues in contact with ASN 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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48A PHE* 3.3 11.0 - - + -
122A SER* 3.4 26.3 + - - +
125A VAL* 4.4 1.8 - - - +
126A GLY* 3.3 35.4 - - - +
283A PHE* 4.5 3.5 - - - +
431A SER 3.5 16.7 + - - +
432A MET* 3.8 15.6 - - + +
433A PHE 3.3 1.0 - - - -
434A GLY* 1.3 76.6 - - - +
436A MET* 1.3 61.8 + - - +
438A GLY* 3.6 7.9 + - - +
439A VAL* 3.8 15.1 - - - +
705A LEU* 3.4 27.6 - - - +
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Residues in contact with MET 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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205A TRP* 4.8 6.1 - - + -
208A LEU* 4.5 18.2 - - + -
212A THR* 4.1 24.0 - - + +
432A MET* 3.3 22.0 + - - +
433A PHE 3.7 5.8 - - - +
434A GLY 3.2 0.6 - - - -
435A ASN* 1.3 74.2 - - - +
437A GLU* 1.3 61.0 + - - +
438A GLY 3.2 0.7 - - - -
439A VAL* 3.4 6.8 + - + +
440A VAL* 3.0 49.8 + - + +
459A THR* 4.3 9.0 - - + +
462A ILE* 3.2 38.4 - - + -
463A CYS* 4.1 20.6 - - - -
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Residues in contact with GLU 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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215A GLY* 4.5 14.3 - - - -
216A ILE* 4.1 12.2 - - - +
284A GLY 5.1 0.7 - - - +
285A GLY* 5.0 4.5 - - - +
288A SER* 4.1 16.3 + - - -
289A PHE* 3.7 32.0 - - + -
292A TYR* 3.1 27.2 + - - -
433A PHE 3.5 5.7 + - - +
434A GLY 3.2 11.7 + - - +
436A MET* 1.3 79.6 - - - +
438A GLY* 1.3 60.1 + - - +
439A VAL 3.4 0.3 + - - -
440A VAL* 4.6 4.9 - - - +
441A VAL* 3.4 40.8 + - + +
442A PRO* 4.0 0.7 - - - +
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Residues in contact with GLY 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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118A SER 4.1 2.4 - - - +
119A MET* 3.8 14.2 - - - -
122A SER* 4.2 13.2 - - - -
283A PHE 4.3 9.5 - - - +
284A GLY 4.7 9.9 - - - -
285A GLY* 4.8 0.6 - - - -
434A GLY 3.3 10.1 + - - -
435A ASN* 3.6 5.1 + - - -
436A MET 3.2 0.8 - - - -
437A GLU* 1.3 79.3 - - - +
439A VAL* 1.3 59.9 + - - +
442A PRO* 3.3 21.0 - - - +
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Residues in contact with VAL 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A MET* 4.2 14.5 - - + +
122A SER* 3.8 27.8 - - - +
123A PHE* 3.9 19.1 - - + +
435A ASN 3.8 13.9 - - - +
436A MET* 3.4 9.8 + - - +
437A GLU 3.2 0.4 - - - -
438A GLY* 1.3 82.4 - - - +
440A VAL* 1.3 64.7 + - + +
441A VAL 3.5 0.2 - - - -
442A PRO* 3.8 2.3 - - - +
443A LEU* 3.3 29.5 + - + +
462A ILE* 4.4 27.6 - - + -
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Residues in contact with VAL 440 (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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436A MET* 3.0 44.0 + - + +
437A GLU* 4.8 6.1 - - - +
439A VAL* 1.3 77.9 - - - +
441A VAL* 1.3 67.9 + - + +
443A LEU* 3.5 4.8 + - - +
444A GLN* 3.1 34.5 + - - +
455A LYS* 5.3 10.5 - - + -
458A LEU* 4.2 15.3 - - + +
459A THR* 4.3 25.4 - - + +
462A ILE* 5.1 6.7 - - + -
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Residues in contact with VAL 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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99A GLY* 4.5 9.6 - - - +
100A SER 5.0 1.6 - - - +
288A SER* 3.7 19.1 - - - +
292A TYR* 4.5 6.5 - - - +
437A GLU* 3.4 48.1 + - + +
440A VAL* 1.3 82.4 - - + +
442A PRO* 1.4 62.8 - - + +
444A GLN* 3.0 25.5 + - + +
445A ASP* 3.2 26.3 + - - +
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Residues in contact with PRO 442 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A SER* 5.3 9.6 - - - +
101A LEU* 3.6 35.4 - - + +
115A GLY 4.4 8.1 - - - +
116A LEU* 6.4 0.2 - - + -
118A SER 5.9 0.4 - - - -
119A MET* 3.8 24.2 - - + -
437A GLU 4.0 0.7 - - - +
438A GLY* 3.3 30.1 - - - +
439A VAL 3.8 1.8 - - - +
441A VAL* 1.4 92.7 - - + +
443A LEU* 1.3 59.6 + - - +
444A GLN 3.2 0.2 - - - -
445A ASP* 3.9 3.8 - - - +
446A LEU* 3.3 28.9 + - - +
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Residues in contact with LEU 443 (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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119A MET* 4.2 17.7 - - + -
439A VAL* 3.3 22.9 + - + +
440A VAL* 3.5 4.9 + - - +
441A VAL 3.2 0.8 - - - -
442A PRO* 1.3 79.4 - - - +
444A GLN* 1.3 58.4 + - - +
446A LEU* 4.1 16.3 + - + -
447A ARG 4.6 1.0 + - - -
448A VAL* 3.6 36.6 - - + +
449A ILE* 4.6 5.5 - - - +
458A LEU* 4.5 12.0 - - + +
462A ILE* 4.0 32.8 - - + -
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Residues in contact with GLN 444 (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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440A VAL* 3.1 26.3 + - - +
441A VAL* 3.0 13.5 + - - +
443A LEU* 1.3 77.2 - - - +
445A ASP* 1.3 65.4 + - - +
446A LEU 3.4 1.1 + - - -
447A ARG* 3.4 27.7 + - - +
449A ILE* 5.0 11.8 - - + +
455A LYS* 4.4 29.0 - - - +
458A LEU* 4.6 14.5 - - + +
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Residues in contact with ASP 445 (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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98A ARG* 3.9 31.9 + - - +
99A GLY* 4.9 5.0 + - - -
101A LEU* 4.4 16.0 + - + +
102A GLY 4.6 7.4 + - - -
441A VAL* 3.2 27.4 + - - +
442A PRO* 3.7 7.9 + - + +
443A LEU 3.5 0.2 - - - -
444A GLN* 1.3 81.1 - - - +
446A LEU* 1.3 60.8 + - - +
447A ARG* 3.3 24.5 + - - +
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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