Contacts of the strand formed by residues 14 - 20 (chain B) in PDB entry 4DI2
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 TYR 14 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6B LEU* 4.5 14.4 - - + -
7B ARG 3.4 9.4 - - - +
13B GLY* 1.3 73.2 - - - -
15B TYR* 1.3 59.8 + - - +
30B LEU* 3.4 7.2 - - - +
31B VAL* 2.8 34.5 + - + +
154B LEU* 3.8 44.2 - - + -
155B CYS 3.7 2.2 + - - -
156B GLY* 2.9 20.8 + - - -
170B VAL* 3.6 22.8 - - + +
171B GLY 3.3 29.4 - - - -
229B SER* 5.2 8.1 + - - +
335B ALA* 4.6 2.9 - - + -
339B GLU* 2.4 33.3 + - - +
502B GOL 3.6 18.6 - - - -
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Residues in contact with TYR 15 (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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5B ASN 3.9 0.5 - - - +
6B LEU* 3.5 9.7 - - - -
7B ARG* 2.8 57.6 + - + +
8B GLY* 3.6 21.3 + - - -
9B LYS* 5.8 0.9 - - - +
13B GLY 4.2 1.3 - - - -
14B TYR* 1.3 75.6 - - - +
16B VAL* 1.3 62.0 + - - +
17B GLU 5.2 0.2 - - - -
28B ASN* 3.4 36.3 - - + -
29B ILE 3.1 22.9 - - - +
30B LEU* 4.0 0.7 - - - +
31B VAL 4.4 0.4 - - - +
113B SER 3.4 24.0 - - - -
114B ASN* 2.8 26.7 + - + +
115B TRP* 3.9 20.4 - + + -
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Residues in contact with VAL 16 (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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5B ASN* 3.9 25.4 - - + +
6B LEU* 3.7 13.0 - - + -
15B TYR* 1.3 76.2 - - - +
17B GLU* 1.3 70.5 + - - +
18B MET* 3.7 22.9 + - + -
28B ASN* 3.6 3.9 - - - -
29B ILE* 2.8 37.5 + - + +
31B VAL* 3.9 6.5 - - + +
87B ILE* 4.0 13.0 - - + -
89B HIS* 5.9 1.1 - - + -
119B LEU* 4.7 3.8 - - + -
174B MET* 3.8 29.4 - - + -
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Residues in contact with GLU 17 (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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5B ASN 4.6 3.0 + - - -
16B VAL* 1.3 76.4 - - - +
18B MET* 1.3 66.9 + - - +
26B THR* 3.7 31.1 + - + +
27B LEU 3.6 4.9 - - - +
28B ASN* 3.9 14.9 + - - +
50B ARG* 5.3 1.2 + - - -
87B ILE* 3.5 13.5 - - - +
88B PRO* 3.4 41.7 - - + +
89B HIS* 4.3 20.4 + - + -
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Residues in contact with MET 18 (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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16B VAL* 4.0 11.0 - - + -
17B GLU* 1.3 80.3 - - - +
19B THR* 1.3 69.7 + - - +
20B VAL* 5.7 1.1 - - + -
26B THR* 3.6 2.8 - - - +
27B LEU* 2.9 31.5 + - + -
29B ILE* 3.7 38.1 - - + -
38B PHE* 3.9 18.4 - - + -
85B VAL* 3.5 27.6 - - + -
86B SER 3.2 8.5 - - - +
87B ILE* 3.8 22.0 - - + -
88B PRO* 3.9 1.8 - - - -
119B LEU* 4.2 17.0 - - + -
136B PHE* 4.0 17.0 - - + -
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Residues in contact with THR 19 (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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18B MET* 1.3 78.7 - - - +
20B VAL* 1.3 63.9 + - - +
21B GLY 5.5 0.3 + - - -
24B PRO* 3.7 28.1 - - + +
25B GLN 3.1 8.3 - - - -
26B THR* 3.9 19.1 - - + +
84B LEU 3.8 0.6 + - - +
85B VAL* 3.3 8.1 - - - +
86B SER* 2.8 50.1 + - - -
88B PRO* 3.9 21.1 - - + -
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Residues in contact with VAL 20 (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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18B MET* 5.7 2.0 - - + -
19B THR* 1.3 78.6 - - - +
21B GLY* 1.3 61.4 + - - +
24B PRO* 4.5 0.2 - - - -
25B GLN* 2.9 40.4 + - + +
27B LEU* 3.8 23.8 - - + -
38B PHE* 4.0 20.6 - - + -
40B VAL* 5.0 5.4 - - + -
52B TYR* 3.5 33.7 - - + -
84B LEU 3.4 3.6 - - - +
85B VAL* 4.0 20.0 - - + -
99B ILE* 4.0 13.7 - - + -
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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