Contacts of the strand formed by residues 20 - 25 (chain C) in PDB entry 1XXF
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 MET 20 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16C ALA* 3.7 8.6 - - + +
17C GLU* 3.0 48.1 + - + +
18C LYS 4.5 3.8 - - - +
19C GLY* 1.3 84.1 + - - +
21C LYS* 1.3 64.0 + - - +
73C VAL* 4.7 9.6 - - + -
74C PHE 3.6 14.1 - - - +
75C ASP* 5.1 4.7 - - + -
118C TYR* 3.7 16.2 - - + +
119C THR* 3.3 39.7 - - - +
120C PRO* 3.9 8.1 - - + -
121C ASP* 3.9 6.3 - - - +
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Residues in contact with LYS 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C ALA* 3.5 11.0 - - - +
20C MET* 1.3 76.9 - - - +
22C ARG* 1.3 60.5 + - - +
23C GLN* 2.9 31.0 + - - +
118C TYR* 3.4 5.2 - - - +
119C THR 2.9 27.8 + - - +
120C PRO 3.2 15.3 - - - +
121C ASP* 2.9 38.1 + - - +
123C VAL 3.5 3.3 + - - -
124C ASP* 3.3 24.9 + - - +
141D VAL* 3.7 28.2 - - + +
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Residues in contact with ARG 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C LEU* 3.6 15.3 - - + +
8C GLU* 3.3 28.9 + - - -
13C TYR* 2.9 21.6 + - - +
14C PRO 2.7 26.8 + - - -
15C GLN* 3.5 13.7 + - - +
16C ALA* 3.6 9.0 - - + +
21C LYS* 1.3 75.2 - - - +
23C GLN* 1.3 61.6 + - - +
116C VAL* 3.6 22.7 - - + -
117C VAL 3.8 2.2 - - - +
118C TYR* 3.3 36.6 - - + -
141D VAL* 3.4 8.1 - - - +
142D ARG* 3.0 57.2 + - - +
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Residues in contact with GLN 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C LYS* 2.9 42.2 + - - +
22C ARG* 1.3 73.3 - - - +
24C VAL* 1.3 61.7 + - - +
25C ILE* 5.6 0.2 - - - -
115C ILE 3.6 1.2 - - - +
116C VAL* 3.3 3.7 - - - +
117C VAL* 2.7 52.0 + - + +
119C THR* 2.9 25.1 + - - +
123C VAL 3.4 8.5 - - - +
124C ASP* 3.8 0.2 - - - -
125C VAL* 3.6 23.7 + - + +
139D ALA* 3.7 27.8 - - + +
140D VAL 3.7 3.4 - - - +
141D VAL* 4.1 13.7 - - + +
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Residues in contact with VAL 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C LEU* 3.5 36.1 - - + -
22C ARG 4.1 0.2 + - - -
23C GLN* 1.3 78.1 - - - +
25C ILE* 1.3 72.2 + - - +
26C GLN* 4.3 1.9 + - + +
114C PRO* 4.1 19.7 - - + -
115C ILE 3.4 1.6 - - - -
116C VAL* 3.8 12.6 - - + -
139D ALA* 4.0 0.2 - - - -
140D VAL* 2.9 38.7 + - - +
142D ARG* 3.3 45.8 - - + +
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Residues in contact with ILE 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C GLN 5.6 0.7 - - - -
24C VAL* 1.3 79.0 - - - +
26C GLN* 1.3 63.1 + - - +
27C LEU* 3.6 30.1 + - + +
40C LEU* 4.3 11.7 - - + -
113C LEU 4.6 0.7 - - - +
114C PRO* 3.5 2.3 - - - +
115C ILE* 2.7 56.2 + - + +
117C VAL* 5.9 2.0 - - + -
125C VAL* 4.2 11.7 - - + -
127C TYR* 3.2 49.4 - - + -
139D ALA* 3.7 21.3 - - + -
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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