Contacts of the strand formed by residues 121 - 125 (chain P) in PDB entry 2XTJ
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 GLY 121 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79P VAL* 6.1 0.2 - - - -
80P VAL 2.9 15.0 - - - -
81P VAL* 4.3 0.2 - - - -
82P LEU* 3.9 13.9 - - - -
91P SER* 3.9 8.0 + - - -
114P VAL* 3.7 6.1 - - - +
115P PHE* 2.9 30.8 + - - +
119P LEU* 3.5 4.9 + - - -
120P PRO* 1.3 74.2 - - - +
122P PHE* 1.3 66.5 + - - +
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Residues in contact with PHE 122 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78P TYR 3.8 0.2 - - - +
79P VAL* 3.7 5.0 - - - +
80P VAL* 2.9 68.0 + - + +
82P LEU* 4.7 3.8 - - + -
91P SER 4.0 8.7 - - - -
94P THR* 3.6 29.6 - - + -
95P ALA* 3.7 32.1 - - + -
98P LEU* 3.8 23.6 - - + -
111P ILE* 4.5 7.0 - - + -
113P HIS 3.3 13.0 - - - +
114P VAL* 4.1 15.7 - - + -
115P PHE* 3.8 8.8 - - - -
121P GLY* 1.3 78.9 - - - +
123P LEU* 1.3 61.2 + - - +
124P VAL* 3.9 13.7 - - + -
137P LEU* 4.6 1.3 - - + -
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Residues in contact with LEU 123 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A ASN* 6.0 0.2 - - - +
262A SER* 3.5 37.0 - - - +
266A ILE* 4.1 19.1 - - + -
77P THR* 3.7 15.5 - - + -
78P TYR 3.6 14.1 - - - +
79P VAL* 4.0 12.3 - - + -
111P ILE* 3.5 4.9 - - - +
112P LEU* 2.8 58.5 + - + -
113P HIS* 2.7 20.1 + - + +
115P PHE* 4.1 11.2 - - + -
122P PHE* 1.3 74.4 - - - +
124P VAL* 1.3 59.5 + - - +
146P ASP* 4.8 0.2 - - - +
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Residues in contact with VAL 124 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77P THR* 3.4 6.0 - - - +
78P TYR* 2.9 46.1 + - + +
80P VAL* 3.8 24.0 - - + -
98P LEU* 4.0 7.6 - - + -
109P THR* 4.0 19.3 - - - -
110P LYS 3.2 10.3 - - - +
111P ILE* 4.1 5.6 - - + -
112P LEU* 5.0 1.1 - - - -
122P PHE* 3.9 13.7 - - + -
123P LEU* 1.3 75.7 - - - +
125P LYS* 1.3 62.7 + - - +
126P MET* 3.8 31.8 + - + -
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Residues in contact with LYS 125 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76P GLY 3.4 14.1 - - - +
77P THR* 4.1 12.1 - - - +
108P LEU* 4.1 1.7 - - - +
109P THR* 3.5 2.4 - - - -
110P LYS* 2.8 72.9 + - + +
112P LEU* 4.3 18.1 - - + +
124P VAL* 1.3 70.8 - - - +
126P MET* 1.3 61.7 - - - +
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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