Contacts of the strand formed by residues 51 - 61 (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 SER 51 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46C LYS 3.8 0.3 - - - +
47C ASN* 4.0 2.5 - - - -
48C ILE* 2.7 49.1 + - - +
49C SER 3.8 0.2 - - - -
50C GLY* 1.3 74.8 - - - +
52C ILE* 1.3 66.4 + - - +
53C GLU* 3.5 3.1 + - - +
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Residues in contact with ILE 52 (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* 4.0 10.3 - - + -
46C LYS 3.5 4.7 - - - -
47C ASN* 4.1 12.1 - - - +
50C GLY 3.4 7.0 + - - +
51C SER* 1.3 72.8 - - - +
53C GLU* 1.3 63.5 + - - +
54C ILE* 4.1 11.8 + - + -
95C PHE* 4.0 33.7 - - + +
403C NDG 4.1 27.8 - - - +
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Residues in contact with GLU 53 (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* 3.4 1.7 - - - -
46C LYS* 2.8 54.9 + - + +
48C ILE* 3.7 21.2 - - + +
51C SER 4.5 4.0 - - - +
52C ILE* 1.3 74.0 - - - +
54C ILE* 1.3 70.3 + - - +
55C VAL* 3.5 6.3 + - + +
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Residues in contact with ILE 54 (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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12C LEU* 6.4 0.2 - - + -
14C PHE* 3.8 38.6 - - + -
16C ALA* 4.0 5.5 - - - +
43C ALA* 6.2 0.2 - - + -
44C THR 3.9 7.0 - - - +
45C TRP* 3.7 4.9 - - + -
52C ILE* 4.1 7.6 - - + -
53C GLU* 1.3 79.1 - - - +
55C VAL* 1.3 63.0 + - - +
56C LYS 4.1 5.6 - - - +
57C GLN* 3.6 28.0 - - - +
95C PHE* 3.6 38.8 - - + -
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Residues in contact with VAL 55 (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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98A VAL* 3.7 42.4 - - + +
14C PHE* 4.3 2.7 - - - -
15C ASN* 4.7 0.2 - - - +
16C ALA* 3.2 33.1 + - + +
17C ASN* 5.0 0.6 + - - +
44C THR* 2.7 18.9 + - + +
45C TRP* 3.8 15.3 - - - +
46C LYS* 4.1 17.3 - - + +
53C GLU* 3.7 13.9 - - + +
54C ILE* 1.3 77.7 - - - +
56C LYS* 1.3 67.8 + - + +
81C VAL* 5.4 1.6 - - + -
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Residues in contact with LYS 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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90A LEU* 4.4 1.8 - - + -
98A VAL* 3.6 33.6 + - + -
99A VAL* 4.4 0.9 - - - +
100A LEU* 3.9 35.9 - - + +
14C PHE 3.2 12.1 - - - +
15C ASN* 2.8 33.7 + - + +
17C ASN* 4.6 4.8 - - - +
21C ASP* 4.3 7.7 + - - -
42C PHE* 3.7 12.0 - - + -
43C ALA* 3.6 1.4 - - - -
44C THR* 2.7 44.7 + - + +
54C ILE* 4.1 3.5 - - - +
55C VAL* 1.3 91.1 + - + +
57C GLN* 1.3 61.8 + - - +
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Residues in contact with GLN 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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100A LEU* 5.9 0.7 - - - +
12C LEU* 3.4 37.1 - - - +
13C PHE* 3.4 8.7 - - - -
14C PHE* 3.0 40.4 + - - +
42C PHE* 3.3 17.0 - - - +
43C ALA* 3.8 9.2 - - + -
54C ILE* 3.6 26.6 - - + +
56C LYS* 1.3 76.0 - - - +
58C GLY* 1.3 59.6 + - - +
92C ASN* 2.6 36.9 + - - +
93C GLU 4.1 2.4 + - - -
95C PHE* 3.8 19.1 - - - -
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Residues in contact with GLY 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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100A LEU* 5.7 1.6 - - - -
11C CYS* 3.7 7.5 - - - +
12C LEU 3.2 12.7 + - - -
13C PHE* 4.5 0.7 - - - -
29C GLU* 3.3 13.2 - - - -
41C CYS* 3.2 9.0 - - - +
42C PHE* 3.0 38.3 + - - -
57C GLN* 1.3 75.6 - - - +
59C CYS* 1.3 59.9 + - - -
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Residues in contact with CYS 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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88A SER* 4.7 1.7 + - - -
100A LEU* 4.7 7.6 - - - +
102A ASN* 5.5 1.7 + - - -
11C CYS* 3.8 2.7 - - - -
29C GLU* 3.1 39.9 + - - +
30C PRO 3.7 0.9 - - - -
31C CYS* 2.1 57.7 - - + -
32C TYR 5.6 0.2 - - - +
40C HIS 3.3 5.2 - - - +
42C PHE* 3.7 11.3 - - - -
58C GLY* 1.3 74.3 - - - -
60C TRP* 1.3 62.6 + - - +
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Residues in contact with TRP 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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34A ALA* 3.8 15.5 - - + -
35A PRO* 4.1 1.1 - - + -
88A SER* 3.5 38.7 + - - +
89A MET 4.2 2.2 - - - -
90A LEU* 3.8 22.7 - - + -
100A LEU* 3.7 24.9 - - + -
39C ARG* 4.1 2.1 - - - +
40C HIS* 2.8 42.2 + - + +
41C CYS 4.3 0.7 - - - -
42C PHE* 3.7 32.5 - + + -
59C CYS* 1.3 76.5 - - - +
61C LEU* 1.3 82.9 + - - +
63C ASP* 2.7 26.8 + - + +
66C CYS* 3.6 24.4 - - - -
83C PHE* 3.9 30.9 - + - -
85C CYS* 4.4 0.2 - - + -
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Residues in contact with LEU 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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86A ALA* 3.8 27.6 - - + +
87A ILE* 3.8 20.4 - - - -
88A SER* 2.8 24.2 + - - +
102A ASN* 3.7 29.8 - - + +
104A GLN* 5.6 0.2 - - - +
32C TYR 4.4 16.8 - - - +
33C GLY* 5.5 4.3 - - - -
38C ARG 5.2 0.4 - - - -
39C ARG* 5.7 0.7 - - - +
40C HIS* 3.5 1.4 + - - -
60C TRP* 1.3 79.4 + - - +
62C ASP* 1.3 71.3 + - + +
63C ASP* 3.0 14.6 + - - +
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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