Contacts of the strand formed by residues 143 - 150 (chain A) in PDB entry 2XKL
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 TYR 143 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A SER* 2.8 36.6 + - - -
59A GLU* 3.2 21.8 - - + +
138A GLU* 4.2 12.6 - - + -
139A THR* 3.5 16.3 + - - -
140A GLY* 3.1 53.7 + - - +
141A GLN 3.7 9.9 - - - -
142A GLY* 1.3 80.4 - - - +
144A GLN* 1.3 66.4 + - - +
145A ARG* 5.0 12.6 - - + -
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Residues in contact with GLN 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ALA* 3.8 6.6 - - - +
55A SER 4.7 0.7 + - - -
59A GLU* 2.8 25.9 + - - +
137A LYS* 3.6 38.0 + - + +
138A GLU 3.3 9.4 - - - +
139A THR* 4.3 3.5 + - - +
143A TYR* 1.3 75.7 - - - +
145A ARG* 1.3 69.3 + - - +
146A PHE* 3.1 31.4 - - + -
172A PHE* 4.1 18.9 - - + -
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Residues in contact with ARG 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A ALA 3.3 11.2 - - - +
54A ALA* 4.2 3.6 - - + +
58A GLU 5.2 1.4 + - - -
59A GLU* 3.0 39.3 + - + +
60A LEU* 4.5 4.5 - - + -
62A THR* 3.7 23.2 - - - +
63A PHE* 3.9 10.5 - - - -
137A LYS* 3.5 5.0 - - - +
138A GLU* 2.9 72.4 + - + +
143A TYR* 5.0 12.0 - - + -
144A GLN* 1.3 78.7 - - - +
146A PHE* 1.3 65.9 + - - +
147A LEU* 3.5 20.6 + - + -
1190A GOL 3.2 24.7 + - - -
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Residues in contact with PHE 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LEU* 3.6 33.4 - - + -
52A GLY* 3.2 6.6 - - - -
53A ALA 2.7 44.0 + - - +
135A MET* 4.5 6.7 - - - -
136A LEU 3.4 3.4 - - - +
137A LYS* 4.1 12.3 - - + -
144A GLN* 3.1 27.4 - - + -
145A ARG* 1.3 74.8 - - - +
147A LEU* 1.3 63.6 + - - +
163A PHE* 3.6 21.0 - - + -
167A THR* 4.3 14.4 - - + -
172A PHE* 3.6 47.3 - + - -
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Residues in contact with LEU 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A LEU* 4.6 7.6 - - + -
49A PHE* 4.0 18.6 - - + -
51A ALA 3.7 1.8 - - - -
52A GLY* 4.7 2.5 - - - -
60A LEU* 5.4 0.2 - - + -
63A PHE* 4.2 8.1 - - + -
134A ILE 3.7 1.0 - - - +
135A MET* 3.3 6.6 - - - +
136A LEU* 2.8 42.3 + - + +
138A GLU* 3.4 34.3 - - + +
145A ARG* 3.5 26.7 - - + -
146A PHE* 1.3 80.4 - - - +
148A LEU* 1.3 60.3 + - - +
149A TYR* 3.8 32.2 + - + +
163A PHE* 4.4 2.2 - - - -
1190A GOL 4.1 0.9 - - - +
1191A POL 4.0 13.2 - - + +
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Residues in contact with LEU 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A PHE* 3.8 0.9 - - - -
50A ILE* 2.8 52.4 + - + +
51A ALA* 2.8 22.6 + - + +
125A LEU* 4.9 0.4 - - + -
126A PHE* 4.1 23.6 - - + -
130A CYS* 4.4 2.7 - - + -
134A ILE 3.7 11.7 - - - +
135A MET* 4.7 1.6 - - + +
147A LEU* 1.3 73.0 - - - +
149A TYR* 1.3 64.9 + - - +
159A CYS* 3.9 26.9 - - - -
160A VAL* 4.4 5.4 - - - -
163A PHE* 3.7 47.8 - - + -
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Residues in contact with TYR 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A LEU* 4.9 2.3 - - - +
47A TRP* 4.0 7.6 - + + -
48A TYR 3.1 9.0 - - - +
49A PHE* 3.8 20.6 - + - -
50A ILE* 4.0 2.5 - - - -
71A PHE* 3.3 36.8 - + + -
73A MET* 4.6 8.5 - - - -
84A LEU* 3.8 8.3 - - + +
133A GLY* 3.4 3.3 - - - -
134A ILE* 2.9 54.1 + - + +
136A LEU* 3.6 29.9 - - + +
147A LEU* 3.8 23.9 - - + +
148A LEU* 1.3 86.6 - - - +
150A ASN* 1.3 63.8 + - - +
1191A POL 2.6 29.5 + - - -
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Residues in contact with ASN 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A TRP* 3.6 6.0 - - - -
48A TYR* 2.8 34.8 + - - +
50A ILE* 3.8 15.0 - - + -
130A CYS 4.5 4.4 - - - -
131A PRO 2.7 28.3 + - - +
132A GLY* 3.3 15.1 - - - +
133A GLY* 3.5 7.9 - - - +
149A TYR* 1.3 74.8 + - - +
151A ARG* 1.3 73.9 + - - +
152A SER* 2.9 30.6 + - - +
155A PRO* 3.6 22.6 - - + +
159A CYS* 4.6 6.8 - - - -
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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