Contacts of the strand formed by residues 39 - 48 (chain C) in PDB entry 2GOO
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 ARG 39 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8C THR* 2.8 56.4 + - - +
9C GLN* 3.9 24.2 - - - +
31C CYS* 2.8 37.4 + - + -
32C TYR* 4.2 7.2 - - - +
33C GLY* 3.8 28.0 - - - +
37C LYS 3.9 5.2 + - - +
38C ARG* 1.3 78.1 - - - +
40C HIS* 1.3 73.6 + - - +
60C TRP 4.3 3.8 - - - +
61C LEU* 6.5 0.4 - - - -
87C GLU* 3.6 5.6 + - - +
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Residues in contact with HIS 40 (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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8C THR* 4.1 2.2 - - - -
11C CYS* 3.6 4.4 - - - -
31C CYS* 4.1 1.7 - - - -
38C ARG* 3.8 12.8 - - + +
39C ARG* 1.3 87.7 - - - +
41C CYS* 1.3 63.2 + - - +
59C CYS* 3.3 8.3 - - - +
60C TRP* 2.8 43.4 + - + +
61C LEU 3.5 9.5 + - - -
62C ASP* 3.5 9.3 - - - -
63C ASP 3.0 42.3 + - - -
66C CYS* 3.6 20.9 - - + +
67C TYR* 3.7 19.7 - + - -
86C CYS 3.1 17.7 - - - +
87C GLU* 3.9 16.0 + - + -
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Residues in contact with CYS 41 (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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8C THR* 3.5 11.2 - - - -
10C GLU 3.8 2.9 - - - -
11C CYS* 2.0 47.6 - - - -
40C HIS* 1.3 73.0 - - - +
42C PHE* 1.3 61.9 + - - +
58C GLY 3.2 5.8 - - - +
60C TRP* 4.3 2.0 - - - -
85C CYS* 3.1 7.2 - - - +
86C CYS* 3.0 28.7 + - - -
91C CYS* 3.4 30.5 - - - -
92C ASN* 3.5 21.5 - - + -
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Residues in contact with PHE 42 (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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90A LEU* 4.0 10.5 - - + -
100A LEU* 3.8 30.1 - - + -
41C CYS* 1.3 76.9 - - - +
43C ALA* 1.3 66.2 + - - +
44C THR* 4.0 8.3 - - + -
56C LYS* 3.7 38.6 - - + -
57C GLN* 3.3 2.7 - - - -
58C GLY* 3.0 45.6 + - - -
59C CYS 3.7 15.7 - - - -
60C TRP* 3.7 14.1 - + + -
72C CYS* 4.8 0.2 - - - -
83C PHE* 3.8 27.4 - + + -
84C CYS 3.2 12.1 - - - +
85C CYS* 4.1 2.5 - - + +
92C ASN* 3.0 22.9 + - - -
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Residues in contact with ALA 43 (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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42C PHE* 1.3 76.8 - - - +
44C THR* 1.3 60.9 + - - +
45C TRP* 3.6 11.8 - - + -
54C ILE* 6.2 0.4 - - + -
56C LYS 3.6 4.5 - - - -
57C GLN* 3.8 15.9 - - + +
72C CYS* 4.1 3.7 - - - -
83C PHE* 3.4 5.5 - - - -
84C CYS* 2.9 47.2 + - - +
92C ASN 4.4 2.7 - - - +
95C PHE* 4.0 17.5 - - + -
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Residues in contact with THR 44 (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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33A VAL* 4.5 0.2 - - - +
90A LEU* 3.7 25.8 - - + +
98A VAL* 4.2 8.4 - - + +
42C PHE* 4.0 5.6 - - + -
43C ALA* 1.3 77.1 - - - +
45C TRP* 1.3 57.6 + - - +
54C ILE* 3.8 2.8 - - - +
55C VAL* 2.7 37.4 + - + -
56C LYS* 2.7 44.7 + - + +
81C VAL* 3.4 17.2 - - - +
82C TYR 2.9 16.9 + - - -
83C PHE* 4.4 1.8 - - - +
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Residues in contact with TRP 45 (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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43C ALA* 3.6 20.2 - - + -
44C THR* 1.3 84.7 + - - +
46C LYS* 1.3 77.5 + - - +
47C ASN* 4.2 2.0 - - + -
52C ILE* 4.0 14.1 - - + -
53C GLU 3.4 14.6 - - - +
54C ILE* 3.7 12.6 - - + +
55C VAL* 3.8 6.5 - - - +
74C GLU* 4.1 10.3 - - + -
81C VAL* 3.7 4.2 - - - +
82C TYR* 2.8 62.9 + + + +
83C PHE 4.3 4.9 - - - -
84C CYS* 3.7 22.7 - - - -
95C PHE* 3.5 36.2 - + - -
96C SER 3.9 16.4 - - - -
403C NDG 3.0 36.7 - - + +
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Residues in contact with LYS 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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92A LEU* 5.6 0.2 - - - +
96A GLU 4.2 16.2 + - - -
97A LYS* 5.8 0.6 - - - +
98A VAL* 4.8 9.3 - - - +
45C TRP* 1.3 80.9 - - - +
47C ASN* 1.3 60.2 + - - +
48C ILE* 4.0 13.9 - - + -
51C SER 3.8 1.4 - - - +
52C ILE* 3.5 2.6 - - - -
53C GLU* 2.8 57.5 + - + +
55C VAL* 4.5 12.0 - - + +
80C GLU* 3.6 17.7 - - - +
81C VAL* 4.0 22.3 - - + +
82C TYR* 4.2 2.5 - - - -
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Residues in contact with ASN 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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45C TRP* 4.6 1.8 - - + -
46C LYS* 1.3 72.5 - - - +
48C ILE* 1.3 61.2 + - - +
49C SER* 3.4 6.5 + - - +
50C GLY 3.2 34.2 - - - +
51C SER 3.5 3.8 + - - -
52C ILE* 4.0 3.2 + - - +
80C GLU 5.3 0.2 + - - -
82C TYR* 3.4 39.4 + - + -
403C NDG 2.4 58.5 + - + +
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Residues in contact with ILE 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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46C LYS* 4.8 11.0 - - + -
47C ASN* 1.3 73.0 - - - +
49C SER* 1.3 65.9 + - - +
50C GLY 3.0 6.9 + - - -
51C SER* 2.7 43.2 + - - +
53C GLU* 3.7 29.6 - - + +
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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