Contacts of the strand formed by residues 99 - 110 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46B SER* 4.4 8.1 - - - +
47B TRP* 3.4 15.0 - - - +
48B LYS* 4.1 15.2 - - + +
93B SER 3.9 0.5 - - - +
94B VAL* 3.5 1.6 - - - -
95B SER* 2.7 48.6 + - - +
97B ASP* 2.6 27.5 + - - -
98B GLY* 1.3 77.2 - - - +
100B VAL* 1.3 67.4 + - - +
101B GLN* 5.8 2.0 - - + -
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Residues in contact with VAL 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B SER* 3.0 29.7 + - - -
47B TRP* 2.7 58.5 + - + +
49B ASP* 4.3 0.9 - - + -
52B LEU* 3.9 24.0 - - + -
71B ILE* 3.6 22.2 - - + -
92B ILE* 3.7 17.5 - - + -
93B SER 3.5 4.7 - - - +
94B VAL* 4.2 6.5 - - + +
98B GLY 4.1 5.6 - - - +
99B THR* 1.3 74.8 - - - +
101B GLN* 1.3 64.9 + - - +
102B TYR 4.1 0.7 - - - -
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Residues in contact with GLN 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B LEU 3.8 1.5 + - - -
46B SER* 3.0 29.0 + - - +
91B ASP* 3.5 3.5 - - - +
92B ILE* 3.3 4.9 - - - -
93B SER* 2.7 49.6 + - - +
95B SER* 5.2 8.3 - - - +
99B THR* 5.6 2.2 - - + -
100B VAL* 1.3 76.7 - - - +
102B TYR* 1.3 60.8 + - - +
145B ASP* 5.5 1.0 + - - -
148B LYS* 3.7 27.0 + - - +
178C ASP* 5.7 0.5 - - - +
179C ARG* 6.3 0.2 - - - +
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Residues in contact with TYR 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B LEU 4.5 1.1 - - - -
44B SER* 3.4 4.7 - - - -
45B LEU* 2.8 65.3 + - + +
47B TRP* 3.6 24.0 - + + -
68B PRO* 5.6 0.4 - - + -
73B ILE* 4.0 34.8 - - + -
85B ARG* 5.1 1.9 + - - -
89B VAL* 3.9 28.7 - - + +
91B ASP 3.7 2.2 - - - -
92B ILE* 3.9 18.4 - - + +
100B VAL* 4.1 1.2 - - + -
101B GLN* 1.3 72.7 - - - +
103B LEU* 1.3 63.5 + - - +
104B GLU* 3.0 48.2 + - + +
148B LYS* 5.4 1.9 + - - -
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Residues in contact with LEU 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B PHE* 3.9 29.8 - - + -
43B LEU 3.6 7.4 - - - +
44B SER* 3.5 27.6 - - - -
89B VAL* 3.7 2.9 - - - +
90B VAL* 2.7 55.0 + - + +
91B ASP* 2.9 23.9 + - + +
101B GLN 5.5 0.4 - - - +
102B TYR* 1.3 79.0 - - - +
104B GLU* 1.3 56.6 + - - +
148B LYS* 5.5 2.7 - - - +
133C ARG* 4.0 31.9 - - - +
177C GLU* 4.1 8.5 - - - +
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Residues in contact with GLU 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B PHE* 3.3 7.8 - - - +
43B LEU* 2.8 57.5 + - + +
85B ARG* 2.6 44.2 + - - -
87B ALA* 3.4 18.3 - - + +
88B ASP 3.2 17.9 - - - +
89B VAL* 4.3 0.7 - - - -
90B VAL* 3.7 3.8 - - - -
102B TYR* 3.0 33.8 + - + +
103B LEU* 1.3 74.3 - - - +
105B ARG* 1.3 63.4 + - - +
106B PHE* 4.0 2.1 - - - +
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Residues in contact with ARG 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B ILE* 3.4 23.5 - - + +
40B ASN* 3.1 34.0 + - - +
41B ALA 3.4 11.0 - - - +
42B PHE* 3.6 25.1 - - + -
86B ASP 4.2 0.2 - - - +
87B ALA* 3.4 1.6 - - - -
88B ASP* 3.0 39.1 + - - +
90B VAL* 3.4 9.1 - - + +
104B GLU* 1.3 75.6 - - - +
106B PHE* 1.3 60.9 + - - +
77C ARG* 4.1 29.1 - - - +
78C PHE 2.6 23.6 + - - +
79C VAL* 2.8 29.4 + - - +
81C VAL* 4.5 5.4 + - - +
84C ALA* 6.0 4.8 - - - +
131C ILE* 5.9 1.0 - - - +
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Residues in contact with PHE 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B ILE* 4.2 10.8 - - + -
39B VAL* 3.8 26.2 - - + -
40B ASN* 3.3 7.2 - - - +
41B ALA* 2.8 78.5 + - + -
42B PHE 4.2 1.8 - - - -
43B LEU* 3.9 23.6 - - + -
78B PHE* 3.2 44.4 - + - -
85B ARG* 3.7 21.1 - - + -
86B ASP 3.3 10.1 - - - +
87B ALA* 4.1 1.6 - - + -
104B GLU* 4.0 5.4 - - - +
105B ARG* 1.3 74.1 - - - +
107B SER* 1.3 67.6 + - - +
108B ALA* 4.1 8.3 - - + -
110B VAL* 6.1 0.4 - - + -
128B ILE* 5.3 2.5 - - + -
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Residues in contact with SER 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B TYR* 4.5 4.3 - - - -
39B VAL 3.1 15.0 - - - -
40B ASN* 3.9 20.2 - - - -
83B ASN* 5.9 0.2 - - - +
86B ASP* 3.0 40.4 + - - +
106B PHE* 1.3 78.8 - - - +
108B ALA* 1.3 61.1 + - - +
82C GLU 3.8 14.5 + - - -
84C ALA* 5.4 6.4 + - - +
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Residues in contact with ALA 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B LYS* 3.5 4.3 - - - -
39B VAL* 3.0 36.5 + - + +
78B PHE* 5.2 1.1 - - + -
81B VAL* 4.2 15.9 - - + -
83B ASN* 3.9 20.6 - - - +
85B ARG* 4.1 15.3 - - + -
106B PHE* 4.1 13.0 - - + -
107B SER* 1.3 75.8 - - - +
109B ARG* 1.3 62.7 + - - +
110B VAL* 3.7 1.2 + - + -
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Residues in contact with ARG 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A SER* 5.7 0.2 + - - -
29B SER* 4.9 2.6 + - - -
31B ASP* 4.5 10.5 + - - +
34B ALA* 3.8 7.3 - - - +
36B THR* 2.5 47.6 + - - +
37B PHE 3.8 3.8 - - - +
38B LYS* 3.7 42.7 - - + +
81B VAL* 3.3 6.3 - - - +
82B GLU* 3.0 51.9 + - - +
83B ASN* 3.7 30.8 - - + +
108B ALA* 1.3 72.1 - - - +
110B VAL* 1.3 61.6 + - - +
402B SO4 3.3 32.9 + - - -
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Residues in contact with VAL 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B THR* 3.2 8.9 - - - -
37B PHE* 2.9 65.7 + - + +
39B VAL* 4.0 23.8 - - + -
80B ASN* 3.4 16.8 - - - +
81B VAL* 4.1 11.9 - - + -
106B PHE* 6.1 0.2 - - + -
108B ALA* 4.1 2.2 - - + +
109B ARG* 1.3 74.8 - - - +
111B LEU* 1.3 63.5 + - - +
112B SER 3.8 1.5 + - - +
127B HIS 3.3 26.9 - - - +
128B ILE* 4.4 11.4 - - + -
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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