Contacts of the strand formed by residues 95 - 99 (chain F) in PDB entry 5ANC
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 HIS 95 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13F LYS 5.1 2.5 + - - -
14F ASN* 6.3 0.7 - - + -
15F LYS 4.4 2.2 - - - -
16F PRO* 3.8 1.8 - - + +
17F TYR* 2.7 41.9 + - + +
59F GLN* 3.5 23.9 + - - -
94F TRP* 1.3 104.7 - - + +
96F VAL* 1.3 75.5 + - - +
97F LEU* 4.3 4.9 - - - +
98F ARG* 5.1 3.8 - - - -
125F THR* 3.5 2.8 - - - +
126F VAL* 2.8 59.4 + - + +
128F ARG* 3.6 31.4 + - + +
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Residues in contact with VAL 96 (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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17F TYR* 2.8 54.9 + - + +
18F ILE* 3.6 8.1 - - - +
19F LYS* 4.2 11.4 - - + -
26F VAL* 3.7 32.1 - - + -
27F PRO* 4.9 2.0 - - + -
94F TRP 4.5 0.9 - - - +
95F HIS* 1.3 93.7 + - - +
97F LEU* 1.3 65.0 + - - +
98F ARG* 4.0 2.1 + - - -
122F PRO* 4.6 5.8 - - + -
124F GLY 3.3 12.8 - - - +
125F THR* 3.7 19.7 - - + +
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Residues in contact with LEU 97 (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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1F MET* 5.0 9.0 - - + -
9F TYR* 3.7 56.5 - - + -
59F GLN* 4.4 11.7 - - - +
61F SER* 5.3 1.3 - - - +
95F HIS* 4.3 10.3 - - - +
96F VAL* 1.3 72.3 - - - +
98F ARG* 1.3 61.2 + - - +
122F PRO* 3.4 3.9 - - - +
123F MET 2.8 38.8 + - - +
124F GLY* 2.8 22.1 + - - +
125F THR 4.6 0.7 - - - +
126F VAL* 3.5 38.6 - - + -
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Residues in contact with ARG 98 (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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9F TYR* 3.3 21.2 + - - -
14F ASN* 4.2 12.9 - - - +
15F LYS* 4.1 13.1 + - - +
17F TYR* 3.5 52.0 - - + +
95F HIS* 5.1 4.8 - - - -
96F VAL 4.0 1.8 + - - -
97F LEU* 1.3 73.2 - - - +
99F ILE* 1.3 61.5 + - - +
100F ASN 4.2 0.2 - - - -
119F PHE* 3.3 41.2 - - - -
120F GLY* 3.7 15.9 - - - +
121F LYS 3.5 4.3 - - - +
1262N A 4.9 6.5 + - - +
1363N G 3.1 28.5 + - - -
1364N G 3.4 26.1 + - - +
1365N U 3.6 12.3 + - - +
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Residues in contact with ILE 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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1F MET* 6.6 0.2 - - + -
3F ARG* 3.8 37.0 + - + +
4F ARG* 3.2 37.2 - - + +
9F TYR* 3.3 22.7 - - + +
98F ARG* 1.3 74.2 - - - +
100F ASN* 1.3 64.4 + - - +
101F LYS* 3.3 10.1 + - + +
120F GLY* 3.5 3.3 - - - -
121F LYS* 2.8 33.5 + - - +
123F MET* 3.4 38.6 - - + +
1365N U 3.4 3.6 - - - -
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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