Contacts of the helix formed by residues 49 - 62 (chain D) in PDB entry 4GQS
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 ASP 49 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46D ASP* 2.9 8.5 + - + +
48D LYS* 1.3 81.2 - - + +
50D VAL* 1.3 64.7 + - - +
51D SER* 3.6 14.2 + - - -
52D LYS* 2.9 40.1 + - + +
53D SER* 3.4 9.0 + - - -
363D PRO* 5.8 0.9 - - - +
473D VAL* 3.6 40.9 - - + +
475D GLY 5.4 3.1 - - - +
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Residues in contact with VAL 50 (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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45D ILE* 4.5 6.1 - - + -
46D ASP 3.5 5.7 + - - -
47D ILE* 4.0 22.0 + - + +
48D LYS 3.9 0.4 + - - -
49D ASP* 1.3 71.1 + - - +
51D SER* 1.3 63.9 + - - +
53D SER* 3.0 21.0 + - - -
54D LEU* 3.2 16.0 + - + +
69D PHE* 4.3 25.8 - - + -
214D GLN* 4.4 17.3 - - + +
364D THR* 4.3 20.2 - - + -
388D LEU* 6.2 0.7 - - + -
475D GLY 5.6 3.8 + - - +
476D PHE* 5.4 10.3 - - + -
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Residues in contact with SER 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D ASP* 3.0 9.6 + - - -
50D VAL* 1.3 79.0 - - - +
52D LYS* 1.3 63.2 + - - +
53D SER 3.1 0.9 + - - -
54D LEU* 3.2 18.9 + - - +
55D THR* 3.2 16.2 + - - -
363D PRO* 2.9 28.5 - - - +
364D THR* 4.8 6.4 - - - +
390D SER* 5.0 4.3 + - - -
392D THR* 2.8 32.9 + - - -
476D PHE 6.0 0.2 - - - -
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Residues in contact with LYS 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D ASP* 2.9 35.4 + - + +
51D SER* 1.3 75.9 - - - +
53D SER* 1.3 52.8 + - - +
55D THR* 3.7 10.3 + - + +
56D ASN* 2.5 62.9 + - - +
59D LYS* 5.3 3.2 - - - +
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Residues in contact with SER 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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45D ILE* 3.7 25.4 - - - -
46D ASP* 3.0 43.3 + - - +
49D ASP 3.4 1.8 + - - -
50D VAL 3.0 11.5 + - - -
52D LYS* 1.3 76.3 - - - +
54D LEU* 1.3 58.3 + - - +
55D THR 3.0 4.5 - - - -
56D ASN* 3.0 8.9 + - - +
57D LEU* 2.8 36.2 + - - +
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Residues in contact with LEU 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D ILE* 4.7 7.4 - - + -
50D VAL* 3.2 21.5 + - + +
51D SER* 3.2 7.4 + - - +
53D SER* 1.3 77.5 - - - +
55D THR* 1.3 59.9 + - - +
57D LEU* 3.9 1.3 - - - -
58D SER* 3.3 19.8 + - - -
65D PHE* 3.6 13.5 - - - -
67D LEU* 3.5 31.6 - - + -
69D PHE* 4.9 5.6 - - + -
76D VAL* 4.0 31.0 - - + -
78D HIS* 3.9 3.8 - - - -
364D THR* 4.1 25.4 - - + -
388D LEU* 4.4 11.9 - - + -
390D SER* 5.1 14.1 - - - -
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Residues in contact with THR 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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51D SER 3.2 15.5 + - - -
52D LYS* 3.8 12.2 - - + +
53D SER 3.0 0.6 - - - -
54D LEU* 1.3 78.1 - - - +
56D ASN* 1.3 64.9 + - - +
57D LEU 3.2 0.4 - - - -
58D SER* 2.6 19.8 + - - -
59D LYS* 3.4 21.1 - - - +
78D HIS* 2.9 34.1 + - + +
390D SER* 4.7 3.1 + - - -
392D THR* 5.0 10.2 - - - +
393D SER* 5.0 1.1 + - - -
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Residues in contact with ASN 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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46D ASP* 5.0 5.5 + - - -
52D LYS* 2.5 51.5 + - - +
53D SER* 3.0 9.6 + - - +
55D THR* 1.3 78.8 - - - +
57D LEU* 1.3 62.6 + - + +
59D LYS* 3.2 43.8 + - + +
60D ILE* 4.1 9.0 - - - +
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Residues in contact with LEU 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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33D PRO* 4.7 8.7 - - + -
44D GLN* 5.7 4.7 - - + +
45D ILE* 3.4 35.9 - - + -
53D SER* 2.8 19.1 + - - +
54D LEU 4.0 4.9 - - - +
56D ASN* 1.3 74.5 - - + +
58D SER* 1.3 52.5 + - - +
59D LYS 2.8 5.2 - - - -
60D ILE* 2.7 36.6 + - + +
61D TYR* 3.2 32.6 + - + -
65D PHE* 4.1 10.1 - - + -
67D LEU* 3.5 31.2 - - + -
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Residues in contact with SER 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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54D LEU 3.3 11.9 + - - -
55D THR 2.6 22.5 + - - -
57D LEU* 1.3 77.0 - - - +
59D LYS* 1.3 57.6 + - - +
60D ILE 3.0 1.7 + - - -
62D GLY* 2.9 48.6 + - - +
65D PHE* 3.8 7.1 - - - -
78D HIS* 3.3 34.4 + - - -
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Residues in contact with LYS 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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52D LYS* 5.3 2.8 - - - +
55D THR* 3.4 23.8 - - - +
56D ASN* 3.2 35.9 + - + +
57D LEU 2.8 0.8 - - - -
58D SER* 1.3 78.1 - - - +
60D ILE* 1.3 63.8 + - + +
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Residues in contact with ILE 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 ASN 4.1 10.8 - - - +
57D LEU* 2.7 20.4 + - + +
59D LYS* 1.3 88.9 - - + +
61D TYR* 1.3 86.6 + - + +
62D GLY 3.8 1.3 - - - -
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Residues in contact with TYR 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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31D PRO* 4.0 18.2 - - + +
32D GLY* 3.3 39.4 + - - -
33D PRO* 3.2 34.3 - - + +
57D LEU* 3.2 29.5 + - + +
60D ILE* 1.3 108.0 - - + +
62D GLY* 1.3 58.3 + - - +
63D PRO* 4.0 0.3 - - - +
64D VAL 3.2 18.2 - - - +
65D PHE* 3.3 26.5 - + + -
379D TYR* 5.5 0.5 + - - -
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Residues in contact with GLY 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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58D SER* 2.9 36.5 + - - -
59D LYS 5.0 0.2 - - - -
60D ILE 3.8 0.8 - - - -
61D TYR* 1.3 81.3 - - - +
63D PRO* 1.3 76.5 - - - +
65D PHE* 3.6 4.5 - - - -
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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