Contacts of the strand formed by residues 98 - 103 (chain F) in PDB entry 4NAW
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 TRP 98 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F ILE* 3.9 12.3 - - + -
17F PRO 2.9 17.5 + - - +
18F THR* 3.3 23.9 - - - +
19F CYS 2.8 25.7 + - - -
39F LEU* 4.1 3.8 - - + -
45F LEU* 5.2 2.9 - - + -
72F TYR* 3.3 27.1 - + + -
77F LEU* 4.0 22.9 - - + -
83F ILE* 4.0 22.4 - - + -
86F LEU* 4.1 14.8 - - + -
87F PHE* 3.6 50.9 - + + -
90F LEU* 5.4 1.1 - - + -
91F ALA* 3.5 22.7 - - + +
95F ALA 5.0 1.8 - - - -
96F LEU* 4.1 2.8 - - - +
97F PRO* 1.3 67.9 - - - +
99F ASN* 1.3 63.5 + - - +
100F ILE* 3.3 30.3 + - + +
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Residues in contact with ASN 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C GLU* 4.5 12.8 + - - +
19F CYS* 3.7 28.0 + - - +
21F THR* 5.1 3.0 + - - -
71F GLU 4.3 1.7 - - - +
72F TYR* 3.2 28.3 - - + -
73F GLU 5.0 1.0 + - - -
95F ALA 4.8 3.1 - - - +
97F PRO* 3.2 18.1 + - - +
98F TRP* 1.3 72.1 - - - +
100F ILE* 1.3 61.6 + - - +
101F THR* 4.1 3.0 + - - -
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Residues in contact with ILE 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F THR* 3.7 20.9 - - + -
19F CYS 3.0 10.3 + - - +
20F PHE* 3.4 30.7 - - + -
21F THR* 3.0 26.1 + - - -
39F LEU* 4.3 4.5 - - + -
45F LEU* 4.4 5.2 - - + -
70F PHE* 3.6 28.9 - - + -
71F GLU 3.7 6.5 - - - +
72F TYR* 5.2 0.4 - - + -
77F LEU* 3.8 15.9 - - + -
98F TRP* 3.3 41.2 + - + +
99F ASN* 1.3 75.3 - - - +
101F THR* 1.3 64.8 + - - +
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Residues in contact with THR 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F THR* 3.3 11.1 - - + +
22F LEU 4.5 0.2 - - - -
23F TYR* 3.7 29.8 - - + -
70F PHE* 3.4 5.0 - - - -
71F GLU* 2.9 54.1 + - - +
99F ASN 4.1 2.5 + - - -
100F ILE* 1.3 72.8 - - - +
102F VAL* 1.3 63.6 + - - +
103F HIS* 3.5 21.7 - - - +
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Residues in contact with VAL 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F PHE* 3.9 25.1 - - + -
21F THR 2.8 16.1 + - - +
22F LEU* 3.6 21.7 - - + +
23F TYR* 2.9 29.5 + - - +
52F VAL* 4.5 0.2 - - + -
56F PHE* 3.7 31.2 - - + -
68F ILE* 3.6 32.5 - - + -
69F TRP 3.8 2.9 - - - +
70F PHE* 4.0 7.6 - - + -
101F THR* 1.3 74.6 - - - +
103F HIS* 1.3 65.2 + - - +
104F PHE* 4.6 3.1 - - + -
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Residues in contact with HIS 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F TYR* 3.2 44.9 - + - -
26F GLU* 3.2 6.9 + - - +
68F ILE* 3.5 9.0 - - - +
69F TRP* 2.8 82.6 + + + +
71F GLU* 2.8 28.2 + - + +
101F THR* 3.5 18.4 - - + +
102F VAL* 1.3 79.0 - - - +
104F PHE* 1.3 67.8 + - - +
105F LYS 4.5 1.8 + - - +
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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