Contacts of the helix formed by residues 45 - 59 (chain C) in PDB entry 1D7G
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 ILE 45 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23C ILE* 3.6 48.9 - - + +
26C LEU* 4.2 14.6 - - + +
27C SER* 3.9 19.3 - - - +
40C PRO* 5.4 6.5 - - + +
41C ASP 5.0 4.3 - - - +
42C LYS* 4.6 15.3 - - + -
43C LEU* 3.0 24.1 - - - +
44C THR* 1.3 86.5 - - - +
46C LEU* 1.3 62.7 + - + +
47C ARG 3.6 1.1 - - - -
48C MET* 3.9 3.4 - - - +
49C ALA* 3.2 24.9 + - - +
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Residues in contact with LEU 46 (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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9A T 5.5 2.2 - - - +
23C ILE* 4.0 26.5 - - + -
26C LEU* 4.3 15.3 - - + -
42C LYS* 5.2 17.5 - - + +
45C ILE* 1.3 72.3 - - + +
47C ARG* 1.3 67.9 + - + +
49C ALA* 3.2 15.4 + - - +
50C VAL* 3.4 18.5 + - - +
18D LYS* 4.5 17.7 - - + -
19D GLU* 4.0 34.1 - - + +
22D VAL* 4.3 29.8 - - + +
23D PHE* 6.0 8.1 - - + -
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Residues in contact with ARG 47 (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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8A C 4.8 6.5 + - - -
42C LYS* 5.9 6.0 - - + +
43C LEU* 4.1 27.5 - - + +
45C ILE* 4.6 0.2 - - - +
46C LEU* 1.3 79.0 - - + +
48C MET* 1.3 60.3 + - + +
50C VAL* 3.2 24.2 - - - +
51C SER* 3.5 9.9 + - - -
18D LYS* 3.3 40.1 - - + +
22D VAL* 6.0 2.0 - - + -
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Residues in contact with MET 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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30C VAL* 6.4 1.8 - - + -
43C LEU* 4.5 26.0 - - + +
44C THR* 3.4 40.4 - - + +
45C ILE 3.9 4.0 + - - +
46C LEU 3.3 0.6 - - - -
47C ARG* 1.3 76.2 - - - +
49C ALA* 1.3 59.1 + - - +
51C SER* 3.6 16.8 - - - -
52C HIS* 2.9 30.0 + - - +
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Residues in contact with ALA 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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26C LEU* 4.1 29.8 - - + -
45C ILE 3.2 16.0 + - - +
46C LEU* 3.2 13.0 + - - +
48C MET* 1.3 75.5 - - - +
50C VAL* 1.3 59.3 + - + +
52C HIS* 3.3 7.6 + - - +
53C MET* 3.0 37.7 + - - +
22D VAL* 5.4 4.5 - - + -
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Residues in contact with VAL 50 (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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46C LEU 3.4 10.7 + - - +
47C ARG* 3.2 23.8 - - - +
49C ALA* 1.3 74.6 - - + +
51C SER* 1.3 56.0 + - - +
53C MET* 3.5 15.8 + - - +
54C LYS* 3.0 40.7 + - + +
22D VAL* 4.4 22.0 - - + +
25D GLU* 3.8 32.1 - - + +
26D LEU 6.1 0.2 - - - +
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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
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47C ARG 3.5 11.2 + - - -
48C MET* 3.5 23.0 + - - -
49C ALA 3.3 0.2 - - - -
50C VAL* 1.3 78.6 - - - +
52C HIS* 1.3 59.7 + - - +
54C LYS* 3.3 12.6 + - - +
55C SER* 3.0 27.6 + - - -
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Residues in contact with HIS 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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29C MET* 5.5 18.0 + - + -
30C VAL* 5.0 17.5 - - + -
48C MET 2.9 18.3 + - - +
49C ALA* 3.6 6.5 + - - +
51C SER* 1.3 71.6 - - - +
53C MET* 1.3 68.8 + - - +
55C SER* 2.7 23.0 + - - -
56C LEU* 3.1 51.3 + - + +
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Residues in contact with MET 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 ALA* 3.0 21.9 + - - +
50C VAL* 3.6 20.4 - - - +
52C HIS* 1.3 78.5 - - - +
54C LYS* 1.3 56.8 + - + +
56C LEU* 3.2 4.0 + - - -
57C ARG* 2.9 53.2 + - - +
25D GLU 5.7 0.2 - - - -
26D LEU* 3.5 36.1 - - + -
29D GLN* 3.2 44.4 - - + +
49D THR* 5.8 1.1 - - + -
53D LEU* 5.9 7.2 - - + -
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Residues in contact with LYS 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 VAL* 3.0 29.8 + - + +
51C SER* 3.5 8.7 - - - +
53C MET* 1.3 73.9 - - + +
55C SER* 1.3 56.5 + - - +
57C ARG* 3.5 9.5 + - - +
58C GLY* 2.9 24.6 + - - -
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Residues in contact with SER 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 10.8 + - - -
52C HIS* 2.7 28.1 + - - -
54C LYS* 1.3 74.7 - - - +
56C LEU* 1.3 63.9 + - - +
58C GLY* 3.3 2.6 + - - -
59C THR* 3.0 33.5 + - - -
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Residues in contact with LEU 56 (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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52C HIS* 3.1 47.0 + - + +
53C MET* 3.2 5.4 + - - +
55C SER* 1.3 84.8 + - - +
57C ARG* 1.3 85.9 + - - +
59C THR* 2.9 32.4 + - - +
53D LEU* 6.2 4.3 - - + -
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Residues in contact with ARG 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 MET* 2.9 45.3 + - - +
54C LYS* 3.5 11.9 - - - +
56C LEU* 1.3 100.8 + - - +
58C GLY* 1.3 62.7 - - - +
59C THR* 3.5 5.0 + - - +
29D GLN* 3.1 33.2 - - - +
53D LEU* 6.0 5.5 - - - +
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Residues in contact with GLY 58 (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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54C LYS 2.9 14.9 + - - -
55C SER* 3.3 5.1 + - - -
57C ARG* 1.3 76.0 - - - +
59C THR* 1.3 60.4 + - - +
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Residues in contact with THR 59 (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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55C SER 3.0 17.7 + - - -
56C LEU* 2.9 26.2 - - - +
57C ARG 3.6 4.7 - - - +
58C GLY* 1.3 80.0 - - - +
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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