Contacts of the strand formed by residues 109 - 114 (chain B) in PDB entry 2XN9
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 THR 109 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B GLN* 3.8 22.4 + - - +
9B SER 4.0 3.9 + - - -
10B PRO* 2.6 29.1 + - + +
11B LYS 3.5 6.1 - - - +
13B LEU* 4.3 22.7 - - + -
23B LEU* 4.4 18.5 - - + +
24B SER 5.1 0.5 + - - -
90B PHE* 3.6 6.0 - - - -
91B TYR* 2.9 33.3 + - - +
108B GLY* 1.3 75.6 + - - -
110B ARG* 1.3 72.0 + - - +
111B LEU* 3.7 1.7 + - + +
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Residues in contact with ARG 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A GLY* 6.4 0.4 - - - -
11B LYS 2.9 14.5 + - - +
12B TYR* 3.6 20.6 + - + -
13B LEU* 2.8 32.9 + - - +
88B THR* 6.4 0.4 - - - +
89B ALA 3.9 8.5 - - - -
90B PHE* 4.1 20.5 - - + -
109B THR* 1.3 72.3 - - - +
111B LEU* 1.3 57.9 + - - +
112B THR* 4.5 5.3 + - - +
153B ASP* 2.6 50.3 + - - +
154B HIS* 3.6 22.0 + - + +
1246B GOL 3.3 14.5 + - - -
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Residues in contact with LEU 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B LEU* 3.2 35.0 - - + +
14B PHE 4.6 0.7 - - - +
15B ARG* 4.7 5.2 - - + -
21B VAL* 4.0 32.5 - - + -
23B LEU* 4.7 6.1 - - + -
80B VAL* 4.3 9.9 - - + -
87B PRO* 3.6 30.5 - - + +
88B THR* 3.1 8.5 - - - +
89B ALA 3.0 31.6 + - - +
91B TYR* 4.0 21.5 - - + -
109B THR* 3.7 1.0 + - + -
110B ARG* 1.3 74.1 - - - +
112B THR* 1.3 68.7 + - - +
113B VAL* 4.2 12.8 - - + -
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Residues in contact with THR 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B LEU 2.9 8.5 + - - +
14B PHE* 3.3 12.8 - - + -
15B ARG 3.2 22.7 + - - -
88B THR* 3.8 12.5 - - + +
110B ARG* 4.5 6.9 + - - +
111B LEU* 1.3 75.4 + - - +
113B VAL* 1.3 66.0 + - - +
151B TYR* 3.7 25.8 - - + +
152B PRO* 4.0 12.9 - - + +
153B ASP 5.3 0.7 + - - +
154B HIS* 2.6 34.9 + - - -
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Residues in contact with VAL 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ARG* 3.3 12.8 - - + +
16B LYS 4.2 1.3 - - - +
17B GLU* 3.7 33.9 - - + +
19B GLN 6.0 1.6 - - - +
21B VAL* 6.1 1.3 - - + -
87B PRO* 3.5 41.5 - - + -
88B THR* 3.0 16.8 + - - +
111B LEU* 4.2 17.3 - - + -
112B THR* 1.3 80.2 - - - +
114B THR* 1.3 63.2 + - - +
115B GLU* 5.8 0.3 - - - +
151B TYR* 4.3 4.2 + - - -
184B ASN* 5.6 1.7 + - - -
185B ASP* 4.9 1.9 - - - +
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Residues in contact with THR 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B PHE* 3.2 34.2 - - + -
15B ARG 2.8 15.2 + - - +
16B LYS* 3.8 9.9 - - - -
17B GLU* 3.0 29.3 + - - +
112B THR 4.0 1.2 + - - -
113B VAL* 1.3 74.5 - - - +
115B GLU* 1.3 57.9 + - - +
116B ASP 2.9 33.4 + - - +
117B LEU* 3.8 5.6 - - + -
119B ASN* 3.4 1.2 + - - +
151B TYR* 3.6 11.3 - - - -
185B ASP* 2.6 23.9 + - - -
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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