Contacts of the helix formed by residues 51 - 63 (chain D) in PDB entry 3G1Q
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 51 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47D GLN 3.4 4.2 + - - -
48D PHE 3.4 2.9 - - - -
50D LYS* 1.3 82.3 - - - +
52D PRO* 1.4 62.3 - - - +
53D LEU 3.4 1.3 - - - -
54D GLY* 3.8 17.2 - - - -
55D PHE* 2.9 26.3 + - - +
457D TYR* 5.2 4.5 - - - -
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Residues in contact with PRO 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D PHE* 3.0 41.6 - - + +
49D GLY* 3.8 5.6 - - - +
50D LYS 3.8 5.6 - - - +
51D SER* 1.4 86.1 - - - +
53D LEU* 1.3 62.8 + - - +
55D PHE* 3.8 0.9 - - + +
56D MET* 3.1 31.4 + - - +
357D LEU* 3.8 22.9 - - + -
385D LEU* 3.7 17.5 - - + -
457D TYR* 3.8 28.3 - - + +
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Residues in contact with LEU 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D SER 3.4 0.6 - - - -
52D PRO* 1.3 80.5 - - - +
54D GLY* 1.3 59.7 - - - +
56D MET* 3.4 3.5 + - - +
57D GLN* 2.9 61.7 + - + +
385D LEU* 3.7 40.9 - - + +
386D LEU* 4.4 8.7 - - + -
389D HIS* 3.7 37.5 - - + +
398D ARG* 4.8 7.9 - - - +
457D TYR* 4.4 13.8 - - + +
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Residues in contact with GLY 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D SER* 3.4 15.6 + - - -
53D LEU* 1.3 78.3 - - - +
55D PHE* 1.3 56.9 + - - +
57D GLN* 3.8 9.6 - - - +
58D GLU* 2.9 32.5 + - - +
61D ARG* 5.0 2.2 + - - -
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Residues in contact with PHE 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D TYR* 4.1 15.9 - + - -
44D HIS* 3.5 34.5 - + + -
47D GLN* 3.5 48.2 - - + +
48D PHE* 3.9 24.5 - + + -
51D SER* 2.9 20.5 + - - +
52D PRO 3.9 2.5 - - - +
54D GLY* 1.3 76.8 - - - +
56D MET* 1.3 61.0 + - + +
58D GLU* 3.4 7.2 + - + +
59D CYS* 3.0 48.3 + - - -
70D ILE* 4.0 20.9 - - + -
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Residues in contact with MET 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D PHE* 3.6 32.8 - - + -
52D PRO* 3.1 18.3 + - - +
53D LEU* 4.0 2.7 - - - +
55D PHE* 1.3 77.3 - - + +
57D GLN* 1.3 65.3 + - - +
59D CYS* 3.4 1.8 + - - -
60D LYS* 3.0 23.9 + - - +
68D PHE* 3.6 12.9 - - + -
79D ILE* 3.5 39.7 - - + -
358D MET* 4.2 5.2 - - - +
383D SER* 3.4 37.0 - - - -
385D LEU* 5.5 2.5 - - - -
386D LEU* 3.6 24.6 - - + +
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Residues in contact with GLN 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D LEU* 2.9 46.4 + - + +
54D GLY* 3.8 7.0 - - - +
56D MET* 1.3 75.1 - - - +
58D GLU* 1.3 65.0 + - - +
60D LYS* 3.0 10.6 + - + +
61D ARG* 2.9 54.3 + - - +
386D LEU* 4.0 16.6 - - + +
389D HIS* 3.9 24.4 + - - +
391D GLU* 6.1 2.6 - - - +
397D PRO* 5.6 2.0 - - - +
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Residues in contact with GLU 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D TYR* 4.2 7.2 - - + +
54D GLY 2.9 19.5 + - - +
55D PHE* 3.5 8.3 - - + +
56D MET 3.3 0.2 - - - -
57D GLN* 1.3 76.7 - - - +
59D CYS* 1.3 61.4 + - - +
61D ARG* 3.7 25.3 + - - +
62D GLN* 3.0 64.8 + - - +
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Residues in contact with CYS 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D TYR* 3.6 39.7 - - + -
55D PHE* 3.0 45.9 + - - -
56D MET 3.6 1.6 - - - +
57D GLN 3.3 0.2 - - - -
58D GLU* 1.3 75.1 - - - +
60D LYS* 1.3 57.9 + - - +
63D LEU* 2.9 37.2 + - + +
68D PHE* 3.2 35.0 - - + -
70D ILE* 4.1 2.2 - - - -
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Residues in contact with LYS 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D MET 3.0 14.7 + - - +
57D GLN* 3.0 10.1 + - + +
59D CYS* 1.3 75.2 - - - +
61D ARG* 1.3 65.0 + - + +
64D LYS* 3.2 15.2 + - - -
65D SER 3.3 25.7 + - - +
66D GLY* 4.0 14.6 - - - +
68D PHE* 3.7 9.4 - - + -
81D GLY 3.1 25.5 + - - +
82D ASP* 5.1 0.6 - - - +
83D PRO* 4.9 0.2 - - - +
386D LEU* 4.5 18.4 + - + +
390D ASP* 2.8 37.3 + - - +
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Residues in contact with ARG 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D GLY* 5.0 2.2 + - - -
57D GLN* 2.9 46.9 + - - +
58D GLU* 3.7 28.9 + - - +
60D LYS* 1.3 76.2 - - + +
62D GLN* 1.3 69.4 + - + +
64D LYS* 2.8 26.3 + - - +
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Residues in contact with GLN 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D TYR* 2.6 40.5 + - + -
58D GLU* 3.0 38.8 + - - +
59D CYS 4.2 1.6 - - - +
61D ARG* 1.3 82.4 - - + +
63D LEU* 1.3 62.7 + - + +
64D LYS* 3.5 8.8 + - - +
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Residues in contact with LEU 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D PRO* 3.9 29.3 - - + +
34D VAL 3.8 17.7 - - - +
35D TYR* 3.9 40.2 - - + +
36D PRO* 4.8 4.3 - - + -
59D CYS 2.9 20.6 + - - +
60D LYS* 5.1 0.2 - - - -
62D GLN* 1.3 76.7 - - + +
64D LYS* 1.3 71.1 + - - +
65D SER* 3.5 7.7 + - - +
68D PHE* 3.7 27.6 - - + -
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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