Contacts of the strand formed by residues 98 - 108 (chain B) in PDB entry 4C02
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 LEU 98 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30B MET 3.5 4.3 - - - +
31B LEU* 3.8 29.2 - - + -
37B PHE* 3.9 11.0 - - + -
75B LEU 3.6 1.6 - - - +
76B THR* 3.5 2.9 - - - +
77B CYS* 2.8 34.6 + - + +
82B ALA* 3.8 24.7 - - + -
83B TYR* 4.1 19.3 - - + -
92B ILE* 3.9 12.6 - - + -
96B ALA* 4.0 18.4 - - + +
97B THR* 1.3 77.9 - - - +
99B ILE* 1.3 62.3 + - - +
100B PHE* 3.9 31.3 - - + -
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Residues in contact with ILE 99 (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 THR 3.7 1.2 - - - +
29B GLY* 3.4 1.4 - - - -
30B MET* 2.7 61.7 + - + +
31B LEU 4.3 13.9 - - - +
32B GLN* 4.7 12.3 - - + +
37B PHE* 4.8 0.3 - - - -
74B LYS* 3.5 40.4 - - + +
75B LEU 3.4 3.6 - - - +
76B THR* 3.6 32.8 - - + +
97B THR* 4.7 5.4 - - + -
98B LEU* 1.3 75.9 - - - +
100B PHE* 1.3 61.3 - - - +
101B ASP 4.2 0.2 - - - -
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Residues in contact with PHE 100 (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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199A LEU* 4.0 19.5 - - + -
27B TYR* 4.2 9.4 - + + -
28B THR 3.3 4.5 - - - +
29B GLY* 3.7 13.9 - - - -
37B PHE* 3.8 28.5 - + - -
57B ILE* 4.1 20.2 - - + -
60B PHE* 3.6 33.0 - + + -
73B ALA 3.5 1.2 - - - +
74B LYS* 3.4 4.1 - - - +
75B LEU* 2.8 49.5 + - + +
77B CYS* 4.2 15.7 - - - -
98B LEU* 3.9 24.0 - - + -
99B ILE* 1.3 76.8 - - - +
101B ASP* 1.3 59.9 + - - +
102B VAL* 3.6 18.1 + - + +
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Residues in contact with ASP 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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8B ILE* 4.1 12.4 - - + +
27B TYR* 3.2 1.2 - - - -
28B THR* 2.8 25.1 + - - +
30B MET* 4.4 14.2 - - + +
41B ARG* 2.9 41.7 + - - +
72B ARG* 2.7 40.2 + - - +
73B ALA 3.7 3.6 - - - -
74B LYS* 4.6 4.7 - - + +
99B ILE 4.2 0.6 - - - -
100B PHE* 1.3 69.9 - - - +
102B VAL* 1.3 60.1 + - - +
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Residues in contact with VAL 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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25B VAL* 4.0 17.7 - - + -
26B HIS 3.3 9.0 - - - +
27B TYR* 4.3 1.6 - - + -
60B PHE* 4.0 19.5 - - + -
64B ALA* 5.5 2.5 - - + -
67B MET* 3.6 20.3 - - - +
72B ARG* 3.2 4.0 - - - +
73B ALA 2.8 36.0 + - - +
75B LEU* 3.7 20.4 - - + -
100B PHE* 3.6 25.8 - - + +
101B ASP* 1.3 81.5 + - - +
103B GLU* 1.3 71.2 + - - +
104B LEU 4.2 0.2 - - - -
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Residues in contact with GLU 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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25B VAL* 3.1 7.4 - - - +
26B HIS* 2.8 42.9 + - + +
41B ARG* 3.9 17.4 + - - +
70B GLY* 4.7 8.2 - - - +
71B GLN 3.5 9.2 - - - +
72B ARG* 4.3 15.0 - - + +
102B VAL* 1.3 77.0 - - - +
104B LEU* 1.3 62.9 + - - +
105B LEU* 3.3 29.4 + - + +
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Residues in contact with LEU 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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17B PRO* 4.3 12.8 - - + -
23B CYS* 4.3 15.5 - - + -
24B VAL 3.9 0.7 - - - +
25B VAL* 3.9 20.4 - - + -
64B ALA* 4.6 4.7 - - + +
67B MET* 3.6 35.9 - - + +
68B SER 3.6 25.4 - - - +
69B LEU* 3.8 8.1 - - + +
70B GLY* 2.8 33.1 + - - -
71B GLN 2.9 15.1 + - - +
103B GLU* 1.3 69.8 - - - +
105B LEU* 1.3 59.4 + - - +
106B ASN 3.7 20.9 - - - +
107B LEU* 4.5 9.6 - - + -
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Residues in contact with LEU 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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24B VAL* 2.8 20.8 + - + +
25B VAL 4.0 1.3 - - - -
26B HIS* 3.6 37.2 - - + +
46B PRO* 4.0 24.5 - - + -
69B LEU* 3.9 6.8 - - - +
70B GLY* 5.1 1.9 + - - -
103B GLU* 3.3 39.5 + - - +
104B LEU* 1.3 74.2 - - - +
106B ASN* 1.3 63.6 + - + +
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Residues in contact with ASN 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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24B VAL* 2.9 43.2 + - + +
69B LEU* 3.5 18.2 - - - +
104B LEU* 3.5 5.4 - - - +
105B LEU* 1.3 82.5 - - + +
107B LEU* 1.3 83.2 + - - +
108B GLU* 3.8 19.8 + - - +
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Residues in contact with LEU 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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15B THR* 4.2 26.0 - - + +
16B PHE 3.9 7.6 - - - +
17B PRO* 3.8 36.8 - - + -
21B GLN* 3.9 27.3 + - + +
22B THR 3.4 7.4 - - - +
23B CYS* 3.8 30.1 - - + -
69B LEU* 4.1 8.3 - - + +
104B LEU* 4.5 11.7 - - + -
106B ASN* 1.3 88.1 + - - +
108B GLU* 1.3 63.0 + - - +
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Residues in contact with GLU 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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20B GLY 4.9 0.5 - - - +
21B GLN* 3.8 16.3 - - - +
22B THR* 3.0 44.7 + - - +
24B VAL* 3.7 26.0 - - + +
48B LYS* 3.4 25.7 + - - -
106B ASN* 3.8 18.6 + - - +
107B LEU* 1.3 77.9 - - - +
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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