Contacts of the helix formed by residues 45 - 57 (chain C) in PDB entry 6VVT
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 LEU 45 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43C GLY 2.6 6.8 + - - -
44C LEU* 1.3 75.2 - - - +
46C ASP* 1.3 60.8 + - - -
47C VAL* 3.4 4.4 + - + -
48C GLN* 3.8 7.5 + - + -
49C THR* 3.5 18.4 + - + +
153C GLU 4.3 4.5 - - - +
154C LYS* 3.4 33.4 - - - +
155C GLY* 4.2 6.7 - - - -
440C LEU* 4.5 6.3 - - + -
443C LYS* 3.4 32.8 - - + -
628C ASP* 3.1 29.8 + - + +
629C ALA* 4.2 9.6 - - - +
630C GLY* 5.0 1.8 - - - +
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Residues in contact with ASP 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C PRO* 6.3 0.9 - - + -
43C GLY* 2.6 44.4 + - - +
44C LEU 3.4 1.2 - - - -
45C LEU* 1.3 69.8 - - - +
47C VAL* 1.3 67.8 + - - +
48C GLN 3.0 3.0 + - - -
49C THR* 3.3 7.6 + - - -
50C ASP* 2.9 56.0 + - - +
60C ARG* 5.2 5.7 + - - -
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Residues in contact with VAL 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C LEU 4.6 4.6 + - - +
45C LEU* 4.8 1.8 - - - -
46C ASP* 1.3 78.9 - - - +
48C GLN* 1.3 71.4 + - + +
50C ASP* 5.0 1.7 - - - +
51C SER* 3.8 19.1 + - - -
168C SER* 4.4 22.7 - - - +
371C THR* 4.7 9.0 - - + +
372C VAL* 4.1 2.3 + - - +
443C LYS* 5.3 0.2 - - + -
444C ARG* 3.9 41.7 - - + +
491C LEU* 4.7 15.3 - - + -
497C VAL* 4.6 20.9 - - + -
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Residues in contact with GLN 48 (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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45C LEU* 3.8 6.7 + - + +
46C ASP 3.1 0.8 - - - -
47C VAL* 1.3 87.5 - - + +
49C THR* 1.3 64.3 + - - +
52C PHE 3.3 3.3 + - - -
151C MET* 3.0 23.9 - - + +
155C GLY* 3.7 32.5 + - - +
157C PHE* 5.0 1.0 - - - -
165C VAL* 4.6 1.3 - - - -
166C VAL 2.7 34.5 + - - +
167C VAL* 4.7 0.3 - - - -
168C SER* 4.5 10.4 + - - -
372C VAL* 3.1 35.9 - - - +
443C LYS* 3.9 31.5 - - + +
444C ARG 4.5 5.7 + - - -
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Residues in contact with THR 49 (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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45C LEU* 3.5 14.6 - - + +
46C ASP* 3.0 20.8 + - - -
48C GLN* 1.3 75.6 - - - +
50C ASP* 1.3 68.2 + - - +
52C PHE* 3.2 1.6 + - - +
53C GLU* 2.7 47.6 + - - +
151C MET* 3.7 15.5 - - - -
152C THR 5.1 2.2 - - - +
153C GLU* 4.5 17.3 - - - +
155C GLY* 4.6 4.9 - - - -
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Residues in contact with ASP 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C ASP* 2.9 47.6 + - - +
47C VAL* 5.0 1.6 - - - +
49C THR* 1.3 81.8 + - - +
51C SER* 1.3 56.5 + - - +
53C GLU* 4.0 10.4 - - - +
54C TRP* 2.8 32.3 + - - +
60C ARG* 4.6 12.0 + - - -
61C TRP* 5.4 1.4 - - - -
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Residues in contact with SER 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C VAL 3.8 8.0 + - - -
48C GLN 3.8 0.4 + - - -
49C THR 3.2 1.0 - - - -
50C ASP* 1.3 79.4 - - - +
52C PHE* 1.3 57.0 + - - +
54C TRP* 3.4 8.5 - - - -
55C LEU 3.0 20.6 + - - -
371C THR* 2.5 36.4 + - - -
372C VAL* 2.9 14.4 + - - -
373C GLY* 2.2 44.6 + - - -
374C GLU* 3.3 0.7 + - - +
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Residues in contact with PHE 52 (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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48C GLN 3.3 3.1 + - - +
49C THR 3.2 1.6 + - - +
51C SER* 1.3 77.1 - - - +
53C GLU* 1.3 63.7 + - + +
55C LEU* 3.1 28.1 + - + +
56C VAL* 2.9 49.6 + - + +
148C PHE* 4.5 4.0 - + - -
149C PRO 3.4 22.4 - - - -
150C MET* 3.7 9.2 - - - -
151C MET* 3.2 56.3 - - + -
157C PHE* 3.4 28.0 - + - -
372C VAL* 3.8 4.0 - - + +
373C GLY* 4.1 4.5 - - - -
376C ILE* 5.6 2.5 - - + -
422C PHE* 5.4 2.9 - + - -
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Residues in contact with GLU 53 (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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49C THR* 2.7 31.6 + - - +
50C ASP* 4.0 7.4 - - - +
52C PHE* 1.3 77.1 - - + +
54C TRP* 1.3 57.5 + - - +
56C VAL* 4.7 2.5 - - - +
57C GLY* 2.8 23.4 + - - -
58C SER* 3.1 36.6 + - - -
60C ARG* 3.8 47.9 + - - +
61C TRP* 4.3 12.0 - - + +
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Residues in contact with TRP 54 (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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50C ASP 2.8 19.6 + - - +
51C SER* 3.4 12.1 - - - +
53C GLU* 1.3 73.4 - - - +
55C LEU* 1.3 86.3 + - - +
57C GLY* 3.3 6.2 + - - -
61C TRP* 3.7 43.3 - + + +
74C VAL 3.8 12.6 + - - -
75C GLY* 3.6 4.3 - - - -
76C GLY* 3.2 16.8 + - - -
79C GLU* 6.0 2.2 - - + -
373C GLY 3.6 5.4 - - - -
374C GLU* 3.2 49.8 - - + -
377C GLN* 3.0 31.2 - - - -
499C PRO 5.5 7.7 + - - -
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Residues in contact with LEU 55 (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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51C SER 3.0 14.8 + - - +
52C PHE* 3.1 32.9 + - + +
54C TRP* 1.3 84.2 - - + +
56C VAL* 1.3 63.7 + - - +
76C GLY* 3.1 12.0 + - - +
77C LEU* 2.8 37.1 - - + +
148C PHE* 4.3 11.0 - - + -
373C GLY* 3.0 25.4 - - - +
376C ILE* 3.3 29.4 - - + -
377C GLN* 3.5 25.4 - - + +
380C ILE* 5.4 2.2 - - + -
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Residues in contact with VAL 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C PHE* 2.9 47.8 + - + +
53C GLU* 4.5 3.4 - - - +
55C LEU* 1.3 73.7 - - + +
57C GLY* 1.3 60.4 + - - +
58C SER* 4.7 8.3 - - - +
77C LEU* 3.5 18.2 - - + +
103C PHE* 4.5 26.1 - - + -
148C PHE* 4.3 15.0 - - + -
150C MET* 4.6 7.4 - - + -
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Residues in contact with GLY 57 (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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53C GLU 2.8 13.6 + - - -
54C TRP 3.7 8.5 - - - -
55C LEU 3.0 3.8 - - - -
56C VAL* 1.3 80.5 - - - +
58C SER* 1.3 66.0 + - - +
59C ASP* 3.7 1.7 + - - +
61C TRP* 3.8 17.0 - - - -
62C ARG* 3.8 14.7 + - - -
75C GLY* 4.4 6.3 - - - -
77C LEU* 5.0 0.2 - - - -
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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