Contacts of the helix formed by residues 430 - 445 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C THR 5.4 0.7 - - - +
47C GLY* 2.9 33.8 + - - +
48C PHE* 3.9 4.2 + - - +
50C VAL* 4.6 2.9 + - - +
223C VAL* 5.6 3.8 - - - +
226C THR* 3.4 30.1 + - - -
227C SER* 5.5 1.6 - - - -
426C CYS 3.2 12.7 + - - -
427C LEU* 3.7 7.8 + - - +
429C LEU* 1.3 78.1 - - - +
431C SER* 1.3 58.9 + - - +
432C MET 3.3 0.2 - - - -
433C PHE* 3.6 29.3 - - - +
434C GLY 4.3 1.0 + - - -
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Residues in contact with SER 431 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C GLY 3.4 5.9 + - - -
48C PHE* 3.5 28.9 + - - +
50C VAL 2.8 27.2 + - - -
51C GLY 4.0 0.3 + - - -
129C TYR* 3.4 24.5 + - - -
427C LEU 3.1 9.3 + - - -
428C GLY 4.5 0.4 - - - -
429C LEU 3.2 0.6 - - - -
430C SER* 1.3 76.2 + - - +
432C MET* 1.3 59.7 + - - +
433C PHE 3.3 1.3 - - - -
435C ASN* 3.5 17.2 - - - +
705C LEU* 3.9 13.4 - - - +
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Residues in contact with MET 432 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C GLY* 3.8 25.4 - - - +
129C TYR* 3.6 26.5 - - + -
130C ASN* 3.8 13.2 - - + +
133C ILE* 4.0 9.9 - - + -
205C TRP* 4.3 4.7 - - + -
208C LEU* 3.7 39.2 - - + +
428C GLY 3.6 15.2 + - - +
429C LEU* 3.1 13.1 + - + +
431C SER* 1.3 76.2 - - - +
433C PHE* 1.3 65.4 + - - +
434C GLY 3.5 0.2 - - - -
435C ASN* 3.8 26.0 - - + +
436C MET* 3.3 26.7 + - - +
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Residues in contact with PHE 433 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C THR* 5.7 2.7 - - + -
208C LEU* 4.4 3.1 - - + -
211C CYS* 3.6 35.0 - - + -
212C THR* 3.6 22.3 - - + +
219C THR* 3.7 29.2 + - + +
222C ALA* 3.5 26.7 - - + -
223C VAL* 4.1 12.6 - - + -
226C THR* 4.5 7.4 - - + -
289C PHE* 4.6 4.4 - - + -
429C LEU* 3.6 34.5 - - + -
430C SER* 3.6 24.5 - - - +
431C SER 3.3 0.6 - - - -
432C MET* 1.3 80.1 - - - +
434C GLY* 1.3 62.5 + - - +
436C MET* 3.4 13.2 + - - +
437C GLU* 3.5 11.1 + - - +
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Residues in contact with GLY 434 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C PHE* 3.4 29.6 - - - +
285C GLY* 4.2 5.5 - - - -
289C PHE* 3.6 30.2 - - - -
430C SER 4.3 1.4 + - - -
433C PHE* 1.3 77.0 - - - +
435C ASN* 1.3 61.9 + - - +
437C GLU* 3.2 12.7 + - - +
438C GLY* 3.3 9.0 + - - -
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Residues in contact with ASN 435 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C PHE* 3.3 11.0 - - + -
122C SER* 3.4 27.1 + - - +
125C VAL* 4.4 2.0 - - - +
126C GLY* 3.3 35.0 - - - +
283C PHE* 4.5 3.5 - - - +
431C SER 3.5 17.4 + - - +
432C MET* 3.8 14.7 - - - +
433C PHE 3.3 0.8 - - - -
434C GLY* 1.3 75.6 - - - +
436C MET* 1.3 61.6 + - - +
438C GLY* 3.6 8.1 + - - +
439C VAL* 3.8 14.6 - - - +
705C LEU* 3.4 28.4 - - + +
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Residues in contact with MET 436 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205C TRP* 4.8 6.3 - - + -
208C LEU* 4.5 19.1 - - + -
212C THR* 4.1 24.2 - - + +
432C MET* 3.3 21.2 + - - +
433C PHE 3.7 5.8 - - - +
434C GLY 3.2 0.2 - - - -
435C ASN* 1.3 75.2 - - - +
437C GLU* 1.3 59.9 + - - +
438C GLY 3.2 0.9 - - - -
439C VAL* 3.4 7.6 + - + +
440C VAL* 3.0 48.5 + - + +
459C THR* 4.3 8.1 - - + +
462C ILE* 3.2 39.0 - - + -
463C CYS* 4.1 20.9 - - - -
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Residues in contact with GLU 437 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215C GLY* 4.5 13.2 - - - -
216C ILE* 4.1 12.5 - - - +
284C GLY 5.1 0.7 - - - +
285C GLY* 5.0 4.5 - - - +
288C SER* 4.1 16.0 + - - -
289C PHE* 3.7 33.1 - - + -
292C TYR* 3.1 26.5 + - - -
433C PHE 3.5 4.9 + - - +
434C GLY 3.2 11.7 + - - +
436C MET* 1.3 79.0 - - - +
438C GLY* 1.3 60.2 + - - +
439C VAL 3.4 0.7 + - - -
440C VAL* 4.1 5.4 - - - +
441C VAL* 3.4 41.4 + - + +
442C PRO* 4.0 0.7 - - - +
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Residues in contact with GLY 438 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C SER 4.1 2.6 - - - +
119C MET* 3.8 14.9 + - - -
122C SER* 4.2 12.3 - - - -
283C PHE 4.3 9.4 - - - -
284C GLY 4.7 10.1 - - - -
285C GLY* 4.8 0.4 - - - -
434C GLY 3.3 9.3 + - - -
435C ASN* 3.6 5.0 + - - -
436C MET 3.2 1.0 - - - -
437C GLU* 1.3 79.2 - - - +
439C VAL* 1.3 60.8 + - - +
442C PRO* 3.3 20.0 - - - +
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Residues in contact with VAL 439 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C MET* 4.2 14.0 - - + +
122C SER* 3.8 27.6 - - - +
123C PHE* 3.9 18.8 - - + +
435C ASN 3.8 13.9 - - - +
436C MET* 3.4 9.3 + - - +
437C GLU 3.2 0.2 - - - -
438C GLY* 1.3 83.0 - - - +
440C VAL* 1.3 64.7 + - + +
441C VAL 3.5 0.9 - - - -
442C PRO* 3.8 2.3 - - - +
443C LEU* 3.3 29.0 + - + +
462C ILE* 4.4 28.5 - - + -
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Residues in contact with VAL 440 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436C MET* 3.0 46.2 + - + +
437C GLU* 4.8 5.6 - - - +
439C VAL* 1.3 77.2 - - - +
441C VAL* 1.3 68.3 + - + +
443C LEU* 3.7 4.0 - - - +
444C GLN* 3.1 34.9 + - - +
455C LYS* 5.3 11.0 - - + -
458C LEU* 4.2 15.6 - - + +
459C THR* 4.3 25.4 - - + +
462C ILE* 5.1 7.2 - - + -
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Residues in contact with VAL 441 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C GLY* 4.5 9.6 - - - -
100C SER 5.0 1.8 - - - +
288C SER* 3.7 18.8 - - - +
292C TYR* 4.5 7.2 - - - +
437C GLU* 3.4 48.2 + - + +
440C VAL* 1.3 82.1 - - + +
442C PRO* 1.4 60.9 - - + +
444C GLN* 3.0 26.3 + - + +
445C ASP* 3.2 26.4 + - - +
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Residues in contact with PRO 442 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C SER* 5.3 8.3 - - - -
101C LEU* 3.6 35.0 - - + +
115C GLY 4.4 9.0 - - - +
116C LEU* 6.4 0.2 - - + -
119C MET* 3.8 24.9 - - + +
437C GLU 4.0 0.7 - - - +
438C GLY* 3.3 29.8 - - - +
439C VAL 3.8 2.0 - - - +
441C VAL* 1.4 94.1 - - + +
443C LEU* 1.3 59.3 + - - +
444C GLN 3.2 0.2 - - - -
445C ASP* 3.9 3.6 - - - +
446C LEU* 3.3 28.9 + - - +
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Residues in contact with LEU 443 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C MET* 4.2 18.1 - - + -
439C VAL* 3.3 23.3 + - + +
440C VAL* 3.5 4.4 + - - +
441C VAL 3.2 0.8 - - - -
442C PRO* 1.3 78.8 - - - +
444C GLN* 1.3 59.8 + - - +
445C ASP 3.5 0.2 - - - -
446C LEU* 4.1 16.5 + - + +
447C ARG 4.6 1.0 + - - -
448C VAL* 3.6 37.2 - - + +
449C ILE* 4.6 5.7 - - - +
458C LEU* 4.5 12.3 - - + +
462C ILE* 4.0 32.1 - - + -
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Residues in contact with GLN 444 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440C VAL* 3.1 26.5 + - - +
441C VAL* 3.0 13.7 + - - +
443C LEU* 1.3 77.0 - - - +
445C ASP* 1.3 64.2 + - - +
446C LEU 3.4 1.1 + - - -
447C ARG* 3.4 26.7 + - - +
449C ILE* 5.0 10.9 - - + +
455C LYS* 4.4 28.4 - - - +
458C LEU* 4.6 14.8 - - + +
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Residues in contact with ASP 445 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C ARG* 3.9 32.8 + - - +
99C GLY* 4.9 4.9 + - - -
101C LEU* 4.4 15.4 + - + +
102C GLY 4.6 7.3 + - - -
441C VAL* 3.2 27.5 + - - +
442C PRO* 3.7 7.5 + - + +
444C GLN* 1.3 80.9 - - - +
446C LEU* 1.3 60.5 - - - +
447C ARG* 3.3 24.7 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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