Contacts of the strand formed by residues 78 - 92 (chain D) 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 CYS 78 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47D CYS* 3.8 4.0 - - - -
76D LYS 5.1 1.3 - - - +
77D ALA* 1.3 76.0 - - - +
79D CYS* 1.3 71.4 + - - +
80D VAL* 3.5 14.5 + - + +
112D GLY 3.3 1.6 - - - +
113D CYS* 3.3 2.4 - - - -
114D ARG* 2.9 42.1 + - - +
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Residues in contact with CYS 79 (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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14D CYS* 2.0 51.6 - - + -
15D LYS 3.6 3.1 - - - -
43D CYS* 3.8 19.6 - - - +
44D HIS* 3.5 22.9 - - - -
45D GLY 3.4 24.6 + - - +
47D CYS* 3.8 3.9 - - - -
78D CYS* 1.3 76.9 - - - +
80D VAL* 1.3 63.8 + - - +
111D CYS* 4.3 1.1 - - - -
112D GLY 3.4 5.2 - - - -
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Residues in contact with VAL 80 (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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43D CYS* 3.5 6.7 - - - -
78D CYS* 4.2 17.9 - - + +
79D CYS* 1.3 79.7 - - - +
81D PRO* 1.3 83.2 - - + +
82D THR* 3.8 0.8 - - + +
111D CYS* 3.4 1.0 - - - -
112D GLY 2.8 33.7 + - - +
114D ARG* 3.7 35.7 - - + +
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Residues in contact with PRO 81 (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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42D TYR* 6.0 0.2 - - - -
43D CYS* 3.4 12.1 - - + +
80D VAL* 1.3 96.7 - - + +
82D THR* 1.3 61.2 + - - +
83D GLU 3.6 0.2 - - - -
84D LEU* 3.9 29.7 - - + +
108D VAL* 3.6 32.3 - - + -
110D GLY 3.3 9.9 - - - +
114D ARG* 5.5 0.7 + - - -
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Residues in contact with THR 82 (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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55D LEU 4.7 1.8 - - - +
56D ASN* 4.6 13.0 + - - -
80D VAL 3.5 2.2 + - - +
81D PRO* 1.3 78.2 - - - +
83D GLU* 1.3 61.0 + - - +
84D LEU* 4.6 3.8 - - - -
110D GLY* 2.8 21.2 + - - -
111D CYS 3.7 5.7 + - - -
112D GLY* 3.6 25.7 - - - +
114D ARG* 3.4 46.2 + - + +
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Residues in contact with GLU 83 (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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81D PRO 3.6 0.4 - - - -
82D THR* 1.3 80.6 - - - +
84D LEU* 1.3 68.2 + - - +
108D VAL* 3.8 0.9 - - - -
109D GLU* 2.8 52.0 + - + +
110D GLY* 3.1 19.5 + - - +
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Residues in contact with LEU 84 (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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81D PRO* 3.9 35.4 - - + +
82D THR 4.6 1.8 - - - -
83D GLU* 1.3 91.7 - - - +
85D SER* 1.3 61.8 + - - +
105D ASP* 3.6 53.6 + - + +
106D MET 5.0 0.7 - - - -
107D VAL 2.9 19.1 - - - +
108D VAL* 4.4 3.8 - - + -
109D GLU* 4.0 4.3 - - - -
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Residues in contact with SER 85 (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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84D LEU* 1.3 74.4 - - - +
86D ALA* 1.3 59.7 + - - +
105D ASP 4.0 4.5 - - - -
106D MET* 2.7 28.8 + - - -
107D VAL* 2.8 26.8 + - - +
109D GLU* 2.5 32.7 + - - -
34F ASP* 4.8 12.1 - - - -
37F LYS* 3.3 18.7 + - - -
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Residues in contact with ALA 86 (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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85D SER* 1.3 79.9 + - - +
87D ILE* 1.3 70.4 + - - +
103D TYR 3.1 15.9 - - - +
104D GLN* 3.8 30.5 - - - +
107D VAL* 5.0 0.2 - - - +
34F ASP* 5.4 2.4 + - - +
37F LYS* 5.3 4.0 + - - +
61F LEU* 3.9 25.1 - - + +
62F ASP* 5.0 3.6 - - - +
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Residues in contact with ILE 87 (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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35D PRO* 4.5 7.0 - - + -
38D TYR* 3.9 37.2 - - + -
86D ALA* 1.3 79.3 - - - +
88D SER* 1.3 64.4 + - - +
89D MET* 3.7 26.9 - - + -
102D ASN* 3.4 1.2 - - - -
103D TYR* 2.8 32.5 + - + +
106D MET* 4.0 23.7 - - + +
107D VAL* 3.7 25.6 - - + -
61F LEU* 3.8 9.6 - - - -
62F ASP 5.0 10.5 - - - +
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Residues in contact with SER 88 (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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35D PRO* 3.6 8.8 - - - +
87D ILE* 1.3 78.2 - - - +
89D MET* 1.3 66.0 + - - +
100D LEU* 4.9 1.1 - - - -
101D LYS 3.5 5.2 - - - -
102D ASN* 2.7 22.5 + - - +
59F CYS 4.8 0.2 + - - -
60F TRP* 3.5 49.0 + - - +
61F LEU* 2.9 30.9 + - - +
62F ASP 5.7 0.2 + - - -
63F ASP* 5.1 0.9 - - - +
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Residues in contact with MET 89 (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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23D PHE* 4.2 14.8 - - - -
28D TRP* 6.2 0.9 - - + -
31D TRP* 5.2 6.3 - - + -
32D ILE* 3.6 33.7 - - + -
34D ALA 3.4 5.8 - - - +
35D PRO* 3.9 6.3 - - + -
87D ILE* 3.7 23.3 - - + -
88D SER* 1.3 80.7 - - - +
90D LEU* 1.3 59.8 + - - +
91D TYR* 4.7 9.5 - - + -
99D VAL 3.8 0.5 - - - +
100D LEU* 3.6 5.5 - - - +
101D LYS* 2.8 31.9 + - - +
103D TYR* 3.8 39.3 - - + +
106D MET* 4.1 11.7 - - - -
60F TRP* 4.0 4.3 - - - -
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Residues in contact with LEU 90 (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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32D ILE* 3.6 2.1 - - - +
33D VAL* 2.8 33.5 + - + -
34D ALA 2.8 21.5 + - - +
89D MET* 1.3 73.1 - - - +
91D TYR* 1.3 61.7 + - - +
98D VAL* 3.7 21.8 - - + -
99D VAL 3.4 12.3 - - - +
100D LEU* 3.8 30.1 - - + -
42F PHE* 4.2 10.8 - - + -
44F THR* 3.6 23.8 - - + +
56F LYS* 4.4 2.9 - - + -
60F TRP* 4.2 5.8 - - + -
83F PHE* 3.4 35.4 - - + -
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Residues in contact with TYR 91 (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 TRP* 3.3 48.2 - + + +
32D ILE* 4.2 10.8 - - + -
33D VAL* 4.1 4.2 - - - +
89D MET* 4.7 7.4 - - + -
90D LEU* 1.3 77.5 - - - +
92D LEU* 1.3 67.6 + - - +
93D ASP* 4.7 6.3 - - + -
98D VAL* 3.3 4.2 - - - -
99D VAL* 2.7 81.3 + - + +
101D LYS* 3.8 23.3 + - + -
103D TYR* 3.1 32.7 + + - -
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Residues in contact with LEU 92 (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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30D ASP 3.7 22.0 - - - +
31D TRP* 2.9 40.6 + - + +
33D VAL* 4.2 9.6 - - + -
91D TYR* 1.3 76.6 - - - +
93D ASP* 1.3 67.0 + - - +
96D GLU* 3.6 31.4 - - + +
97D LYS 3.3 1.8 - - - -
98D VAL* 3.6 28.3 - - + -
80F GLU* 6.1 0.9 - - - +
81F VAL* 4.2 18.2 - - + -
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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