Contacts of the strand formed by residues 110 - 115 (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 LYS 110 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99P GLN* 4.5 0.9 - - - +
108P LEU* 4.3 23.3 - - + +
109P THR* 1.3 73.2 - - - +
111P ILE* 1.3 64.2 + - - +
112P LEU* 3.4 19.6 + - + -
124P VAL* 3.2 4.5 - - - -
125P LYS* 2.8 82.7 + - + +
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Residues in contact with ILE 111 (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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95P ALA* 4.1 34.1 - - + +
98P LEU* 4.9 2.2 - - + -
99P GLN* 3.4 30.9 - - - +
109P THR* 4.2 6.7 - - - +
110P LYS* 1.3 74.7 - - - +
112P LEU* 1.3 64.9 + - - +
113P HIS* 4.2 6.0 - - - +
114P VAL* 4.0 26.7 - - + -
122P PHE* 4.5 8.7 - - + -
123P LEU 3.6 9.0 - - - +
124P VAL* 4.1 20.2 - - + -
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Residues in contact with LEU 112 (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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77P THR* 4.4 11.0 - - + +
110P LYS* 4.2 31.6 - - + +
111P ILE* 1.3 73.7 - - - +
113P HIS* 1.3 61.5 + - - +
123P LEU* 2.8 42.0 + - + +
125P LYS* 4.3 22.7 - - + +
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Residues in contact with HIS 113 (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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266A ILE* 3.7 50.3 - - + +
269A GLU* 2.8 30.8 + - - -
111P ILE* 3.4 3.6 + - - +
112P LEU* 1.3 83.4 + - - +
114P VAL* 1.3 81.4 + - - +
115P PHE* 3.8 14.0 + + - -
122P PHE* 3.3 3.3 - - - +
123P LEU* 2.7 39.9 + - + +
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Residues in contact with VAL 114 (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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269A GLU* 4.0 0.5 - - - +
88P LEU* 3.8 25.5 - - + +
91P SER* 4.0 14.8 - - - -
92P GLU* 4.1 24.5 - - + +
95P ALA* 5.1 2.5 - - + -
111P ILE* 4.0 18.8 - - + -
113P HIS* 1.3 92.5 + - - +
115P PHE* 1.3 65.3 + - - +
116P HIS* 3.3 6.2 + - - +
121P GLY 3.7 11.9 - - - +
122P PHE* 4.1 7.0 - - + -
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Residues in contact with PHE 115 (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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262A SER 4.6 1.6 - - - -
265A LEU* 3.7 42.4 - - + -
266A ILE* 3.8 25.8 - - + -
269A GLU* 3.2 21.1 - - - +
79P VAL* 3.8 20.9 - - + -
88P LEU* 4.3 4.7 - - - +
91P SER* 4.8 2.1 + - - -
113P HIS* 3.8 7.4 - + - -
114P VAL* 1.3 74.3 - - - +
116P HIS* 1.3 64.6 + - - +
118P LEU* 5.7 2.0 - - + -
119P LEU* 3.3 39.2 - - + +
120P PRO* 4.2 2.4 - - - +
121P GLY 2.9 23.8 + - - +
122P PHE* 3.8 25.4 - - - -
123P LEU* 4.1 14.4 - - + -
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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