Contacts of the strand formed by residues 90 - 100 (chain C) in PDB entry 3BX7
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 GLY 90 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40C ARG* 4.6 2.2 - - - -
41C GLN 3.8 8.7 - - - -
42C ALA* 4.6 4.5 - - - -
88C ASP 3.3 4.4 + - - -
89C THR* 1.3 77.7 - - - +
91C LEU* 1.3 59.2 + - - -
92C TYR* 3.4 10.9 - - - -
113C GLN* 3.4 14.4 - - - +
114C ILE 2.8 32.3 + - - -
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Residues in contact with LEU 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C ALA 5.3 0.2 - - - +
39C LEU 3.3 4.0 - - - +
40C ARG* 3.5 0.3 - - - -
41C GLN* 2.8 70.6 + - + +
90C GLY* 1.3 71.2 - - - -
92C TYR* 1.3 58.7 + - - +
93C ILE* 3.6 15.4 + - + +
110C ASN 3.7 17.7 - - - +
111C GLY 3.6 26.2 - - - +
112C THR 3.7 0.4 - - - -
113C GLN* 3.5 25.9 + - + +
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Residues in contact with TYR 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C GLN* 3.1 11.3 + - - -
21C PHE* 4.6 8.6 - - + -
38C VAL* 3.9 17.9 - - + -
39C LEU 3.4 3.8 - - - -
40C ARG* 3.5 16.7 - - + -
49C VAL* 4.0 24.0 - - + -
67C ILE* 5.6 0.7 - - + -
81C ILE* 3.7 23.8 - - + -
84C LEU* 3.5 25.6 - - + +
88C ASP* 2.7 31.4 + - - +
90C GLY* 3.4 21.1 - - - -
91C LEU* 1.3 71.8 - - - +
93C ILE* 1.3 58.5 + - - +
112C THR* 2.7 40.3 + - - +
114C ILE* 3.5 30.7 - - + -
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Residues in contact with ILE 93 (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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7C GLN* 3.8 2.9 - - - -
37C THR 3.3 5.4 - - - +
38C VAL* 3.4 3.8 - - - -
39C LEU* 2.8 56.1 + - + +
41C GLN* 4.0 28.5 - - + +
46C VAL* 6.1 2.2 - - + -
91C LEU* 4.1 17.7 - - + +
92C TYR* 1.3 72.7 - - - +
94C CYS* 1.3 64.5 + - - +
95C LYS 4.7 0.4 - - - +
108C ILE* 3.6 21.8 - - + -
109C GLY 3.4 21.5 - - - +
110C ASN 4.4 1.1 - - - +
111C GLY* 3.8 16.6 - - - +
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Residues in contact with CYS 94 (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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5C VAL* 4.0 9.8 - - + +
7C GLN* 3.1 15.7 + - - +
21C PHE* 4.3 3.4 - - - -
23C CYS* 2.0 52.9 - - + -
36C VAL* 4.4 8.5 - - + -
37C THR 3.8 2.7 - - - -
38C VAL* 4.7 4.9 - - - +
79C LEU* 3.8 20.0 - - - -
93C ILE* 1.3 75.2 - - - +
95C LYS* 1.3 59.4 + - - +
96C VAL* 4.0 4.7 - - + -
108C ILE* 3.5 2.6 - - - -
109C GLY 3.0 26.2 + - - -
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Residues in contact with LYS 95 (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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72A SER* 4.6 9.9 - - - +
73A HIS* 4.3 25.3 - - - +
35C ARG* 3.5 2.4 - - - +
36C VAL* 3.3 4.3 - - - +
37C THR* 2.8 58.6 + - - +
39C LEU* 4.6 19.5 - - + +
48C GLU* 5.5 0.6 + - - -
93C ILE 3.7 0.2 + - - -
94C CYS* 1.3 74.2 - - - +
96C VAL* 1.3 62.1 + - - +
97C GLU* 3.8 33.3 + - + +
106C LEU* 4.2 16.2 - - + -
107C GLY 3.6 3.8 - - - +
108C ILE* 4.1 24.5 - - + +
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Residues in contact with VAL 96 (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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3C MET* 3.4 25.6 - - + +
5C VAL* 4.3 19.5 - - + -
23C CYS* 5.2 2.5 - - + -
25C TYR* 3.8 34.8 - - + -
34C VAL* 3.6 28.0 - - + -
35C ARG 3.5 3.6 - - - +
36C VAL* 4.4 13.7 - - + -
54C TYR* 4.5 1.3 - - - +
94C CYS* 4.7 3.1 - - + -
95C LYS* 1.3 77.3 - - - +
97C GLU* 1.3 61.6 + - - +
98C LEU* 5.0 0.4 - - + -
106C LEU* 3.2 2.8 - - - -
107C GLY 2.9 36.6 + - - +
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Residues in contact with GLU 97 (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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70A ILE* 4.7 4.7 - - - +
72A SER* 4.8 1.7 + - - -
34C VAL* 3.3 5.9 - - - +
35C ARG* 2.9 75.3 + - - +
37C THR* 4.1 3.6 + - - -
95C LYS* 3.8 29.9 + - + +
96C VAL* 1.3 75.6 - - - +
98C LEU* 1.3 63.4 + - - +
99C MET* 3.3 18.0 + - - +
104C TYR* 2.5 37.1 + - + +
105C TYR 3.6 2.7 - - - -
106C LEU* 3.6 15.8 - - + +
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Residues in contact with LEU 98 (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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40A ARG* 3.9 34.1 - - + +
3C MET* 4.2 26.9 - - + -
25C TYR* 5.4 2.0 - - + -
26C ALA 5.8 0.9 - - - +
28C PRO* 5.2 6.3 - - + -
32C THR* 3.9 17.5 - - + -
33C GLU 3.9 5.2 - - - -
34C VAL* 4.3 17.7 - - + -
96C VAL* 5.0 0.4 - - + -
97C GLU* 1.3 73.5 - - - +
99C MET* 1.3 63.0 + - - +
100C TYR 3.6 2.2 - - - -
101C PRO 5.1 1.9 - - - +
103C PRO 4.2 5.9 - - - +
104C TYR* 3.6 10.8 - - - -
105C TYR* 2.8 55.9 + - + +
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Residues in contact with MET 99 (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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77A GLU* 5.2 3.8 - - + +
79A THR* 3.8 42.1 + - + +
33C GLU* 2.9 23.9 + - + +
34C VAL 4.8 0.7 - - - -
35C ARG* 3.5 58.3 - - + +
53C THR* 5.3 3.4 - - + -
97C GLU* 3.7 24.9 - - - +
98C LEU* 1.3 73.6 - - - +
100C TYR* 1.3 66.4 + - + +
101C PRO 4.8 3.2 - - - -
102C PRO* 5.2 1.2 - - - +
104C TYR* 4.0 17.9 - - + +
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Residues in contact with TYR 100 (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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80A ILE 3.8 17.0 - - - -
81A ALA* 3.7 28.9 - - + -
82A THR 5.2 1.4 + - - -
94A LEU* 3.2 19.6 - - + +
95A GLY 4.9 1.0 + - - -
96A ASN* 2.6 29.0 + - - -
100A TYR* 3.2 27.1 - - - -
31C ALA 5.1 1.8 - - - -
32C THR* 3.2 8.6 - - - +
33C GLU* 2.7 59.0 + - + +
98C LEU 3.6 1.0 - - - -
99C MET* 1.3 81.1 - - + +
101C PRO* 1.3 84.4 + - + +
102C PRO* 4.5 1.1 - - + -
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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