Contacts of the helix formed by residues 49 - 62 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46B ASP* 3.1 19.8 + - - +
47B ILE 2.9 1.6 - - - -
48B LYS* 1.3 88.8 - - + +
50B VAL* 1.3 65.2 + - - +
51B SER* 3.9 6.4 + - - -
52B LYS* 3.2 38.1 + - + +
53B SER* 3.3 14.7 + - - -
473B VAL* 3.0 33.8 - - + +
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Residues in contact with VAL 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B ILE* 4.6 10.0 - - + +
46B ASP 3.5 7.3 + - - -
47B ILE* 4.0 6.1 + - - +
49B ASP* 1.3 73.2 - - - +
51B SER* 1.3 73.2 + - - +
53B SER* 2.9 16.5 + - - -
54B LEU* 3.0 23.1 + - + +
69B PHE* 5.4 11.2 - - + -
214B GLN* 5.4 7.0 - - - +
363B PRO* 5.0 3.4 - - + -
364B THR* 4.0 26.5 - - + +
388B LEU* 6.1 2.0 - - + -
473B VAL* 5.5 3.1 - - + -
475B GLY 3.4 23.8 + - - +
476B PHE* 4.6 11.4 - - - +
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Residues in contact with SER 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B ASP* 3.5 6.0 + - - -
50B VAL* 1.3 85.1 - - - +
52B LYS* 1.3 62.0 + - - +
54B LEU* 3.1 9.5 + - - +
55B THR* 3.0 27.0 + - - -
363B PRO* 3.7 18.7 + - - -
364B THR* 4.5 6.9 - - - +
390B SER* 4.4 5.4 + - - -
392B THR* 2.8 43.2 + - - +
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Residues in contact with LYS 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B ASP* 3.2 36.2 + - + +
50B VAL 3.2 0.8 + - - -
51B SER* 1.3 77.7 - - - +
53B SER* 1.3 60.1 + - - +
55B THR* 3.7 4.9 + - - -
56B ASN* 2.9 61.9 + - - +
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Residues in contact with SER 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B GLN 4.8 1.1 + - - -
45B ILE* 3.5 26.4 - - - -
46B ASP* 2.8 37.4 + - - +
49B ASP 3.3 1.9 + - - -
50B VAL 2.9 10.3 + - - -
52B LYS* 1.3 78.4 - - - +
54B LEU* 1.3 60.0 + - - +
56B ASN* 3.2 9.8 + - - +
57B LEU* 2.8 33.7 + - - +
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Residues in contact with LEU 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B ILE* 4.8 6.3 - - + -
50B VAL* 3.0 24.8 + - + +
51B SER* 3.1 6.9 + - - +
53B SER* 1.3 75.7 - - - +
55B THR* 1.3 55.2 + - - +
57B LEU* 2.7 28.6 + - + +
58B SER* 2.8 18.1 + - - -
65B PHE* 4.1 5.5 - - + -
67B LEU* 3.5 32.8 - - + -
69B PHE* 5.4 3.4 - - + -
76B VAL* 4.0 28.3 - - + -
78B HIS* 4.6 4.5 - - + -
364B THR* 3.6 31.0 - - + -
388B LEU* 5.0 7.9 - - + -
390B SER* 4.8 9.2 - - - +
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Residues in contact with THR 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B SER* 3.0 20.1 + - - -
52B LYS* 3.8 7.0 - - + -
54B LEU* 1.3 75.3 - - - +
56B ASN* 1.3 73.5 + - - +
58B SER* 3.3 4.2 + - - -
59B LYS* 3.2 34.3 + - - +
78B HIS* 2.9 35.8 + - + +
390B SER* 4.9 2.1 + - - -
392B THR* 5.3 4.0 - - - +
393B SER* 5.0 3.8 + - - -
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Residues in contact with ASN 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B LYS* 2.9 52.2 + - - +
53B SER* 3.5 11.7 - - - +
54B LEU 3.1 0.4 - - - -
55B THR* 1.3 83.2 - - - +
57B LEU* 1.3 58.2 + - - +
59B LYS* 3.1 41.3 - - - +
60B ILE* 4.0 10.0 - - - +
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Residues in contact with LEU 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B PRO* 3.7 30.1 - - + -
44B GLN* 5.6 10.3 - - + +
45B ILE* 4.3 11.2 - - + -
53B SER* 2.8 21.2 + - - +
54B LEU* 2.7 18.0 + - + +
56B ASN* 1.3 74.0 - - - +
58B SER* 1.3 50.2 + - - +
59B LYS 2.9 4.5 - - - -
60B ILE* 2.7 27.2 + - + +
61B TYR* 3.1 24.1 + - + -
65B PHE* 3.6 15.7 - - + -
67B LEU* 3.5 37.0 - - + -
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Residues in contact with SER 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B LEU 2.8 13.5 + - - -
55B THR 3.6 8.5 - - - -
57B LEU* 1.3 76.1 - - - +
59B LYS* 1.3 57.3 + - - +
60B ILE 2.9 2.9 + - - -
61B TYR* 3.7 1.3 - - - +
62B GLY* 2.9 45.3 + - - +
65B PHE* 3.4 13.8 - - - -
78B HIS* 3.0 42.1 - - - +
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Residues in contact with LYS 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B THR* 3.2 25.5 + - - +
56B ASN* 3.1 34.4 - - - +
57B LEU 2.9 0.2 - - - -
58B SER* 1.3 76.2 - - - +
60B ILE* 1.3 62.1 + - + +
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Residues in contact with ILE 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B ASN 4.0 10.5 - - - +
57B LEU* 2.7 9.1 + - + +
59B LYS* 1.3 88.0 - - + +
61B TYR* 1.3 88.7 + - + +
62B GLY 3.7 1.1 - - - -
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Residues in contact with TYR 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B PRO* 4.1 17.7 - - + +
32B GLY* 3.3 39.7 + - - -
33B PRO* 3.5 36.2 - - + +
57B LEU* 3.1 27.4 + - + +
60B ILE* 1.3 109.1 - - + +
62B GLY* 1.3 61.8 + - - +
63B PRO* 4.7 0.2 - - - +
64B VAL 3.5 15.8 - - - +
65B PHE* 3.5 20.8 - + + +
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Residues in contact with GLY 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B SER* 2.9 36.9 + - - -
60B ILE 3.7 1.0 - - - -
61B TYR* 1.3 81.7 - - - +
63B PRO* 1.3 71.7 - - - +
65B PHE* 4.1 3.1 - - - -
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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