Contacts of the helix formed by residues 2449 - 2462 (chain F) in PDB entry 6X34
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 GLY2449 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2448F LYS* 1.3 77.2 - - - +
2450F GLU* 1.3 61.1 + - - +
2451F ALA 3.5 1.7 - - - +
2452F LEU* 3.7 23.8 + - - +
2453F ARG* 4.3 5.4 + - - +
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Residues in contact with GLU2450 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2448F LYS* 3.0 11.0 + - + +
2449F GLY* 1.3 78.9 - - - +
2451F ALA* 1.3 61.7 + - - +
2452F LEU 3.4 0.7 + - - -
2453F ARG* 3.7 33.0 + - - +
2454F ILE* 4.5 3.5 + - - +
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Residues in contact with ALA2451 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2439F PRO* 3.9 25.1 - - + +
2444F ILE* 3.3 29.8 + - + +
2448F LYS* 4.7 1.8 - - + +
2449F GLY 4.5 1.4 - - - +
2450F GLU* 1.3 76.4 - - - +
2452F LEU* 1.3 57.8 + - - +
2453F ARG 3.2 1.3 - - - -
2454F ILE* 3.2 15.2 - - + +
2455F ARG* 2.9 30.8 + - - +
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Residues in contact with LEU2452 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2444F ILE 5.2 0.6 + - - -
2449F GLY* 3.7 21.9 + - - +
2450F GLU 3.2 1.4 - - - -
2451F ALA* 1.3 78.3 - - - +
2453F ARG* 1.3 58.2 + - - +
2455F ARG* 3.5 13.8 - - - +
2456F ALA* 2.9 31.2 + - - +
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Residues in contact with ARG2453 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174D VAL* 3.8 16.0 + - - +
175D SER* 3.3 27.3 + - - +
176D SER* 4.6 3.4 - - - +
177D GLU* 3.9 27.2 - - + +
2449F GLY 4.3 4.3 + - - +
2450F GLU* 3.7 25.1 + - - +
2451F ALA 3.2 0.2 - - - -
2452F LEU* 1.3 80.1 - - - +
2454F ILE* 1.3 72.1 + - + +
2456F ALA* 3.3 4.8 + - - +
2457F ILE* 2.9 40.0 + - + +
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Residues in contact with ILE2454 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2348F GLU 5.9 0.7 - - - +
2351F ALA* 5.7 2.2 - - + -
2352F ASN* 5.0 16.8 - - + +
2355F VAL* 4.7 26.0 - - + -
2437F CYS 5.4 3.4 - - - +
2439F PRO* 3.6 26.7 - - + -
2450F GLU 4.8 2.7 - - - +
2451F ALA* 3.2 19.2 + - + +
2453F ARG* 1.3 96.2 - - + +
2455F ARG* 1.3 60.3 + - - +
2457F ILE* 3.5 10.9 - - + +
2458F LEU* 2.9 35.7 + - + +
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Residues in contact with ARG2455 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2439F PRO* 3.7 26.8 + - + +
2440F GLU* 5.4 1.6 - - - +
2445F GLN* 3.4 31.8 - - - +
2451F ALA* 2.9 19.5 + - - +
2452F LEU* 3.5 13.3 - - - +
2454F ILE* 1.3 78.2 - - - +
2456F ALA* 1.3 58.5 + - - +
2458F LEU* 3.2 17.8 - - + +
2459F ARG* 2.9 31.9 + - + +
2509F ARG 5.4 3.2 + - - -
2510F VAL* 3.6 23.1 + - - +
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Residues in contact with ALA2456 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2452F LEU 2.9 17.1 + - - +
2453F ARG* 3.7 5.2 - - - +
2455F ARG* 1.3 77.8 - - - +
2457F ILE* 1.3 65.4 + - + +
2459F ARG* 4.0 5.1 - - - +
2460F SER* 2.9 27.9 + - - -
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Residues in contact with ILE2457 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D LEU* 3.7 25.1 - - + -
133D PHE* 5.8 5.4 - - + -
176D SER* 4.2 17.5 - - - +
177D GLU* 6.3 0.4 - - + -
195D PHE* 3.9 15.5 - - + -
2355F VAL* 6.3 2.2 - - + -
2359F ILE* 4.1 32.1 - - + -
2453F ARG* 2.9 29.7 + - + +
2454F ILE* 3.5 12.6 - - + +
2455F ARG 3.2 0.4 - - - -
2456F ALA* 1.3 77.2 - - + +
2458F LEU* 1.3 63.9 + - + +
2460F SER* 2.8 20.2 + - - +
2461F LEU* 3.1 15.0 - - + +
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Residues in contact with LEU2458 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2355F VAL* 5.4 11.2 - - + -
2434F LEU* 4.8 22.6 - - + +
2437F CYS 4.6 2.9 - - - +
2438F ALA* 3.7 30.3 - - + +
2439F PRO* 3.8 7.2 - - + -
2454F ILE* 2.9 25.7 + - + +
2455F ARG* 3.2 20.6 - - + +
2457F ILE* 1.3 79.2 - - + +
2459F ARG* 1.3 65.3 + - + +
2461F LEU* 3.7 18.6 + - - +
2462F VAL* 4.0 6.6 + - - +
2506F PHE* 5.2 7.0 - - + -
2510F VAL* 3.6 36.6 - - + +
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Residues in contact with ARG2459 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2455F ARG* 2.9 22.8 + - + +
2456F ALA* 4.0 5.8 - - - +
2458F LEU* 1.3 80.4 - - + +
2460F SER* 1.3 63.5 + - - +
2461F LEU 3.3 0.2 - - - -
2462F VAL 3.4 16.5 - - - +
2463F PRO* 3.8 3.6 - - - +
2506F PHE* 6.1 0.7 - - - -
2510F VAL* 5.7 4.7 - - + +
2511F TYR* 3.1 42.6 + - + +
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Residues in contact with SER2460 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D LYS* 4.6 8.8 - - - +
131D LEU* 3.2 29.2 - - - +
133D PHE* 6.2 3.8 - - - -
2456F ALA 2.9 15.1 + - - -
2457F ILE* 2.8 19.6 + - - +
2459F ARG* 1.3 76.8 - - - +
2461F LEU* 1.3 65.2 + - - +
2463F PRO* 4.3 9.1 - - - +
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Residues in contact with LEU2461 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D LYS* 5.1 0.9 - - + -
131D LEU* 3.5 31.4 - - + -
2359F ILE* 5.0 9.2 - - + -
2365F PHE* 4.9 28.0 - - + -
2370F ARG* 4.5 20.9 - - + -
2377F LEU* 5.6 2.3 - - - +
2434F LEU* 5.3 8.5 - - + -
2457F ILE* 3.1 32.1 + - + +
2458F LEU* 3.9 11.0 - - - +
2459F ARG 3.3 0.2 - - - -
2460F SER* 1.3 83.7 + - - +
2462F VAL* 1.3 70.5 + - + +
2463F PRO* 3.3 7.8 - - - +
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Residues in contact with VAL2462 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2377F LEU* 4.3 22.7 - - + -
2431F ILE* 3.7 29.8 - - + -
2434F LEU* 5.8 5.8 - - + -
2458F LEU 4.0 3.9 + - - +
2459F ARG* 3.4 10.3 + - - +
2461F LEU* 1.3 87.7 - - + +
2463F PRO* 1.3 68.6 - - - +
2466F ASP* 3.6 25.8 - - + -
2467F LEU 4.9 2.0 - - - +
2503F MET* 6.6 0.2 - - + -
2506F PHE* 4.0 23.4 - - + -
2511F TYR* 3.9 10.6 - - - -
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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