Contacts of the helix formed by residues 55 - 67 (chain C) in PDB entry 4GGF
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 ASN 55 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51C LYS 4.8 4.0 - - - +
52C GLU* 2.9 17.2 + - - +
53C ASN 3.2 1.5 - - - -
54C LYS* 1.3 79.9 - - + +
56C GLU* 1.3 64.6 + - - +
57C LYS* 3.0 23.3 + - - +
58C VAL* 2.9 32.1 + - + +
59C ILE* 3.3 4.9 + - - +
99L GLU* 2.9 29.9 + - - +
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Residues in contact with GLU 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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38C LYS* 2.7 41.6 + - + +
53C ASN 4.7 2.3 + - - -
54C LYS 4.0 2.2 + - - -
55C ASN* 1.3 72.4 + - - +
57C LYS* 1.3 59.6 + - + +
59C ILE* 3.2 9.9 + - + +
60C GLU* 2.9 32.1 + - - +
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Residues in contact with LYS 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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55C ASN* 3.0 10.6 + - - +
56C GLU* 1.3 75.0 - - + +
58C VAL* 1.3 64.8 + - - +
60C GLU* 3.4 21.1 + - - +
61C HIS* 3.0 22.7 + - - +
99L GLU* 3.0 47.8 + - + +
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Residues in contact with VAL 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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52C GLU* 3.9 33.2 - - + +
55C ASN* 2.9 38.8 + - + +
57C LYS* 1.3 73.9 - - - +
59C ILE* 1.3 62.3 + - - +
61C HIS* 3.1 4.3 + - + +
62C ILE* 2.9 35.7 + - + +
97L GLY* 4.3 14.4 - - - +
98L ASP 4.0 14.6 - - - +
99L GLU* 4.0 13.7 - - + -
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Residues in contact with ILE 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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37C PHE* 3.8 20.5 - - + -
38C LYS* 3.8 32.8 - - + +
41C VAL* 3.9 23.8 - - + -
49C LEU* 5.1 0.7 - - + -
52C GLU* 3.6 42.4 - - + +
53C ASN* 4.0 11.9 - - - +
55C ASN 3.3 4.0 + - - +
56C GLU* 3.2 11.3 + - + +
58C VAL* 1.3 76.2 - - - +
60C GLU* 1.3 61.7 + - - +
62C ILE* 3.3 14.7 + - + +
63C MET* 3.0 19.4 + - - +
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Residues in contact with GLU 60 (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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34C GLN* 3.4 29.9 + - - +
38C LYS* 2.8 30.6 + - - +
56C GLU* 2.9 25.3 + - - +
57C LYS* 3.7 24.2 - - - +
58C VAL 3.2 0.2 - - - -
59C ILE* 1.3 75.5 - - - +
61C HIS* 1.3 59.1 + - - +
63C MET* 3.4 5.4 + - - +
64C GLU* 3.0 27.5 + - - +
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Residues in contact with HIS 61 (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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57C LYS 3.0 11.2 + - - +
58C VAL* 3.1 6.5 + - + +
60C GLU* 1.3 73.1 - - - +
62C ILE* 1.3 70.5 + - + +
64C GLU* 3.2 11.0 + - - +
65C ASP* 2.9 34.5 + - + +
26K PHE* 3.8 30.5 - + - -
27K HIS* 5.5 0.8 - + - -
95L HIS* 4.3 13.2 + + - +
98L ASP* 3.1 62.8 + - + +
99L GLU 4.3 6.7 - - - -
100L GLY* 4.3 5.3 + - - +
102L GLY 4.6 5.4 + - - -
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Residues in contact with ILE 62 (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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37C PHE* 4.0 12.3 - - + -
49C LEU* 4.6 13.5 - - + -
52C GLU* 4.4 12.3 - - + -
58C VAL* 2.9 34.2 + - + +
59C ILE* 3.7 22.9 - - + +
61C HIS* 1.3 85.8 - - + +
63C MET* 1.3 62.1 + - - +
65C ASP* 3.3 7.3 + - + +
66C LEU* 3.1 40.6 + - + +
82C LEU* 4.2 16.8 - - + -
85C ARG* 6.0 1.3 - - - +
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Residues in contact with MET 63 (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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32C LEU 3.8 11.4 - - - +
34C GLN* 3.7 34.3 - - + +
37C PHE* 3.7 46.4 - - + -
59C ILE 3.0 9.6 + - - +
60C GLU* 3.7 8.7 - - - +
61C HIS 3.2 0.2 - - - -
62C ILE* 1.3 76.6 - - - +
64C GLU* 1.3 63.5 + - - +
66C LEU* 3.1 5.3 + - - -
67C ASP* 2.9 24.5 + - + +
72C LYS* 3.3 34.8 - - - +
73C GLN* 4.0 2.9 - - - -
74C LEU* 3.7 15.1 - - + +
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Residues in contact with GLU 64 (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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60C GLU 3.0 16.8 + - - +
61C HIS* 3.2 13.9 + - - +
63C MET* 1.3 75.6 - - - +
65C ASP* 1.3 63.1 + - - +
67C ASP* 3.3 12.6 + - + +
25K ASN* 2.9 16.6 + - - -
26K PHE* 3.6 30.2 - - + -
100L GLY* 5.5 2.3 - - - -
101L PRO* 5.3 1.6 - - - +
102L GLY* 4.1 19.9 + - - -
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Residues in contact with ASP 65 (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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61C HIS* 2.9 26.0 + - - +
62C ILE* 3.5 9.0 - - - +
63C MET 3.2 0.2 - - - -
64C GLU* 1.3 78.4 - - - +
66C LEU* 1.3 56.1 + - - +
68C THR* 4.4 4.7 - - - +
85C ARG* 2.8 35.9 + - - -
25K ASN* 2.9 19.5 + - - +
26K PHE* 3.6 15.7 - - + -
27K HIS* 2.9 35.6 + - - +
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Residues in contact with LEU 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C PHE* 4.1 6.7 - - + -
62C ILE* 3.1 34.5 + - + +
63C MET 3.1 5.3 + - - +
65C ASP* 1.3 76.4 - - - +
67C ASP* 1.3 57.7 + - - +
68C THR* 3.0 14.6 + - - +
74C LEU* 3.8 27.4 - - + -
78C GLU* 3.2 39.9 - - - +
79C PHE* 5.2 1.6 - - - -
81C MET* 4.1 3.8 - - + -
82C LEU* 3.8 37.9 - - + +
85C ARG* 3.8 28.7 - - - +
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Residues in contact with ASP 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C MET* 2.9 18.0 + - + +
64C GLU* 3.7 9.8 - - + +
65C ASP 3.2 1.6 - - - -
66C LEU* 1.3 72.2 - - - +
68C THR* 1.3 61.8 + - - +
69C ASN* 3.1 6.4 - - - +
70C ALA* 3.1 15.2 + - - +
71C ASP* 3.1 4.7 + - - +
72C LYS* 2.8 34.0 + - - +
73C GLN 3.8 5.6 - - - -
74C LEU* 3.7 10.8 - - + -
78C GLU* 4.0 1.3 - - - -
203C CA 2.3 31.3 - - - -
25K ASN* 3.1 13.8 + - - +
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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