Contacts of the strand formed by residues 99 - 110 (chain C) in PDB entry 5J0Z
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 THR 99 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46C SER* 4.4 8.5 - - - +
47C TRP 3.3 15.5 - - - +
48C LYS* 4.1 15.0 - - + +
93C SER 4.0 0.2 - - - +
94C VAL* 3.5 1.5 - - - -
95C SER* 2.7 50.0 + - - +
97C ASP* 2.6 27.1 + - - -
98C GLY* 1.3 78.2 - - - +
100C VAL* 1.3 68.9 + - - +
101C GLN* 5.8 2.0 - - + -
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Residues in contact with VAL 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C SER* 3.0 29.3 + - - -
47C TRP* 2.6 58.6 + - + +
49C ASP* 4.3 0.7 - - + -
52C LEU* 3.9 23.8 - - + -
71C ILE* 3.6 22.9 - - + -
92C ILE* 3.7 17.3 - - + -
93C SER 3.6 4.5 - - - +
94C VAL* 4.2 6.3 - - + +
98C GLY 4.1 6.1 - - - +
99C THR* 1.3 76.9 - - - +
101C GLN* 1.3 64.4 + - - +
102C TYR 4.0 0.9 - - - -
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Residues in contact with GLN 101 (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 LEU 3.8 1.0 + - - -
46C SER* 3.0 29.2 + - - +
91C ASP* 3.5 2.9 - - - +
92C ILE* 3.3 4.9 - - - -
93C SER* 2.7 49.3 + - - +
95C SER* 5.1 9.2 - - - +
99C THR* 5.5 2.0 - - + -
100C VAL* 1.3 76.4 - - - +
102C TYR* 1.3 59.6 + - - +
145C ASP* 5.3 1.2 + - - -
148C LYS* 3.7 27.9 + - - +
178D ASP* 5.1 6.9 - - - +
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Residues in contact with TYR 102 (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 LEU 4.5 0.9 - - - -
44C SER* 3.4 5.7 - - - -
45C LEU* 2.8 65.0 + - + +
47C TRP* 3.6 23.3 - + + -
73C ILE* 4.0 34.8 - - + -
85C ARG* 5.2 2.3 + - - -
89C VAL* 3.9 30.0 - - + +
91C ASP 3.7 2.0 - - - -
92C ILE* 3.9 18.4 - - + +
100C VAL* 4.0 1.4 - - + -
101C GLN* 1.3 73.1 + - - +
103C LEU* 1.3 63.5 + - - +
104C GLU* 3.0 48.4 + - + +
148C LYS* 5.4 1.6 + - - -
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Residues in contact with LEU 103 (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* 3.9 25.4 - - + -
43C LEU 3.6 8.1 - - - +
44C SER* 3.5 27.6 - - - -
89C VAL* 3.8 2.6 - - - +
90C VAL* 2.7 49.5 + - + +
91C ASP* 2.9 23.9 + - + +
101C GLN 5.5 0.2 - - - +
102C TYR* 1.3 78.2 - - - +
104C GLU* 1.3 57.3 + - - +
148C LYS* 5.5 2.0 - - - +
133D ARG* 3.7 35.7 - - - +
177D GLU* 3.7 13.9 - - - +
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Residues in contact with GLU 104 (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* 3.3 7.7 - - - +
43C LEU* 2.8 61.8 + - + +
85C ARG* 2.6 45.0 + - - -
87C ALA* 3.4 17.4 - - - +
88C ASP 3.2 18.6 - - - +
89C VAL* 4.3 0.4 - - - +
90C VAL* 3.7 3.8 - - - -
102C TYR* 3.0 31.0 + - + +
103C LEU* 1.3 74.9 - - - +
105C ARG* 1.3 59.3 + - - +
106C PHE* 4.0 2.4 - - - +
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Residues in contact with ARG 105 (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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25C ILE* 3.4 26.2 - - + +
40C ASN* 3.1 32.9 + - - +
41C ALA 3.5 11.4 - - - +
42C PHE* 3.6 22.0 - - + -
86C ASP 4.2 0.2 - - - +
87C ALA* 3.4 2.1 - - - -
88C ASP* 3.0 38.3 + - - +
90C VAL* 3.4 9.8 - - + +
104C GLU* 1.3 74.8 - - - +
106C PHE* 1.3 62.0 + - - +
77D ARG* 4.1 32.5 - - - +
78D PHE 2.7 23.4 + - - -
79D VAL* 2.8 30.2 + - - +
81D VAL* 4.7 3.4 + - - +
84D ALA* 6.3 1.0 - - - +
131D ILE* 5.7 1.6 - - - +
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Residues in contact with PHE 106 (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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22C ILE* 4.2 10.3 - - + -
39C VAL* 3.9 26.2 - - + -
40C ASN* 3.3 6.8 - - - +
41C ALA* 2.8 78.4 + - + +
42C PHE 4.1 2.2 - - - -
43C LEU* 3.9 22.9 - - + -
78C PHE* 3.2 44.2 - + - -
85C ARG* 3.7 24.7 - - + -
86C ASP 3.3 9.4 - - - +
87C ALA* 4.1 1.1 - - + -
104C GLU* 4.0 4.7 - - - +
105C ARG* 1.3 75.3 - - - +
107C SER* 1.3 67.2 + - - +
108C ALA* 4.1 5.4 - - + -
110C VAL* 6.1 0.4 - - + -
128C ILE* 5.3 2.2 - - + -
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Residues in contact with SER 107 (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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28C TYR* 4.5 4.3 - - - -
39C VAL 3.2 14.6 - - - -
40C ASN* 3.9 20.9 - - - -
83C ASN* 5.9 0.3 - - - +
86C ASP* 3.0 39.0 + - - +
106C PHE* 1.3 79.2 - - - +
108C ALA* 1.3 61.1 + - - +
82D GLU 3.9 15.3 + - - -
84D ALA* 5.4 5.8 + - - +
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Residues in contact with ALA 108 (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* 3.5 5.5 - - - -
39C VAL* 3.0 35.7 + - + +
78C PHE* 5.1 0.9 - - + -
81C VAL* 4.2 16.8 - - + -
83C ASN* 3.9 20.4 - - - +
85C ARG* 4.1 15.0 - - + -
106C PHE* 4.1 13.1 - - + -
107C SER* 1.3 75.5 - - - +
109C ARG* 1.3 62.4 + - - +
110C VAL* 3.7 1.6 + - + -
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Residues in contact with ARG 109 (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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403B SO4 3.6 37.8 + - - -
31C ASP* 4.3 5.3 + - - +
34C ALA* 3.7 11.7 - - - +
36C THR* 3.4 40.2 + - - +
37C PHE 3.8 5.6 - - - +
38C LYS* 3.7 38.6 - - + +
81C VAL* 3.3 6.6 - - - +
82C GLU* 3.2 50.6 + - + +
83C ASN* 3.7 31.0 + - + +
108C ALA* 1.3 73.6 - - - +
110C VAL* 1.3 61.2 + - - +
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Residues in contact with VAL 110 (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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36C THR* 3.2 8.8 - - - -
37C PHE* 2.9 61.4 + - + +
39C VAL* 4.0 26.7 - - + -
80C ASN* 3.4 17.0 - - - +
81C VAL* 4.1 12.3 - - + -
82C GLU* 5.5 0.4 - - - -
106C PHE* 6.1 0.4 - - + -
108C ALA* 4.2 2.2 - - + +
109C ARG* 1.3 76.5 - - - +
111C LEU* 1.3 63.2 + - - +
112C SER 3.7 1.7 + - - +
127C HIS 3.3 26.9 - - - +
128C ILE* 4.4 11.9 - - + -
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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