Contacts of the strand formed by residues 66 - 75 (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 VAL 66 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A PHE* 5.0 0.2 - - + -
62A THR 4.5 4.3 - - - +
63A PHE* 3.0 35.1 + - + +
64A ASP 3.2 0.2 - - - -
65A PRO* 1.3 79.8 - - + +
67A ASP* 1.3 62.3 + - - +
68A ASN 3.4 17.9 - - - +
69A ILE* 3.7 32.3 - - + -
88A ILE* 3.9 21.5 - - + -
89A ARG 3.8 4.3 - - - +
91A LYS* 3.5 11.3 - - - -
176A LEU* 6.2 0.2 - - - +
178A THR* 3.8 16.8 - - + +
179A PRO* 3.3 18.7 - - - +
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Residues in contact with ASP 67 (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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65A PRO 3.6 3.0 + - - -
66A VAL* 1.3 74.6 - - - +
68A ASN* 1.3 82.7 + - - +
89A ARG* 2.8 17.4 + - + +
90A THR 4.0 6.7 - - - +
91A LYS* 3.7 5.7 - - + +
178A THR* 3.5 11.1 - - - -
179A PRO* 3.6 11.8 - - + +
180A ARG* 3.0 27.7 + - - -
181A ASN* 2.8 30.7 + - - +
182A GLN* 3.0 41.3 + - - +
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Residues in contact with ASN 68 (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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48A TYR* 5.5 4.1 - - + -
49A PHE 5.3 0.2 - - - -
66A VAL* 3.4 3.1 - - - +
67A ASP* 1.3 103.2 + - - +
69A ILE* 1.3 75.9 + - - +
70A VAL 4.3 0.7 + - - -
87A THR 5.0 0.3 - - - +
88A ILE* 3.7 0.2 - - - -
89A ARG* 2.8 40.7 + - - +
178A THR* 4.8 2.9 - - - -
180A ARG* 3.8 20.2 - - + -
182A GLN 3.3 7.6 + - - -
183A GLU 3.2 22.0 + - - -
184A ALA* 3.4 23.7 - - - +
185A CYS 4.3 1.0 + - - -
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Residues in contact with ILE 69 (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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48A TYR* 3.3 11.4 - - - +
49A PHE* 3.2 57.9 + - + +
63A PHE* 4.7 4.5 - - + -
66A VAL* 3.7 22.0 - - + -
68A ASN* 1.3 84.3 - - - +
70A VAL* 1.3 63.8 + - - +
71A PHE* 4.2 7.9 - - + -
86A ALA* 3.8 25.1 - - + -
87A THR 3.8 11.2 - - - +
88A ILE* 4.0 22.9 - - + -
100A TRP* 4.8 4.0 - - + -
1191A POL 4.1 17.7 - - + -
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Residues in contact with VAL 70 (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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46A LEU* 4.0 25.4 - - + -
47A TRP 3.6 5.6 - - - +
48A TYR* 3.7 28.0 - - + +
68A ASN* 4.3 1.4 + - - -
69A ILE* 1.3 73.8 - - - +
71A PHE* 1.3 65.7 + - - +
86A ALA* 3.3 1.4 - - - +
87A THR* 2.9 41.5 + - - +
184A ALA* 4.2 6.5 - - + -
185A CYS 3.3 34.8 - - - +
187A LEU* 4.0 16.3 - - + +
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Residues in contact with PHE 71 (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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46A LEU* 3.4 4.0 - - - -
47A TRP* 2.7 60.1 + - + +
48A TYR 3.9 2.9 - - - -
49A PHE* 3.8 25.6 - - + -
69A ILE* 4.2 14.1 - - + -
70A VAL* 1.3 79.5 - - - +
72A ASN* 1.3 63.7 + - - +
73A MET* 3.8 15.5 - - + -
84A LEU* 3.8 22.9 - - + -
85A ARG 3.1 16.8 - - - +
86A ALA* 3.7 11.7 - - + -
149A TYR* 3.3 50.3 - + - -
187A LEU* 3.7 7.9 - - - -
1191A POL 4.5 7.0 - - - -
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Residues in contact with ASN 72 (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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43A HIS 5.7 2.2 - - - +
45A GLY 3.6 19.1 - - - +
46A LEU* 4.7 4.5 - - + +
47A TRP* 4.7 1.3 - - - -
71A PHE* 1.3 75.6 - - - +
73A MET* 1.3 68.7 + - - +
74A ALA* 4.8 2.4 - - - +
83A GLN 3.6 0.6 + - - +
84A LEU* 3.4 6.1 - - - -
85A ARG* 3.0 56.3 + - - +
187A LEU* 3.7 20.1 - - + +
188A SER 4.7 6.8 - - - +
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Residues in contact with MET 73 (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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42A PRO* 3.3 44.4 + - + +
43A HIS* 3.1 38.9 + - + +
45A GLY 4.9 0.4 + - - -
47A TRP* 3.7 21.4 - - + +
71A PHE* 3.8 23.1 - - + -
72A ASN* 1.3 78.5 + - - +
74A ALA* 1.3 61.3 + - - +
82A LEU* 4.2 19.7 - - + -
83A GLN 3.5 4.7 - - - -
84A LEU* 4.0 11.2 - - + -
134A ILE* 5.1 9.2 - - + -
136A LEU* 5.2 4.3 - - - -
149A TYR* 4.6 13.5 - - - -
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Residues in contact with ALA 74 (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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43A HIS* 4.2 5.6 - - - +
72A ASN* 5.0 4.3 - - - +
73A MET* 1.3 75.8 - - - +
75A ALA* 1.3 68.3 + - - +
76A GLY 3.5 0.2 + - - -
82A LEU* 3.5 9.4 - - - +
83A GLN* 2.8 34.8 + - + +
85A ARG* 3.9 24.5 - - - +
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Residues in contact with ALA 75 (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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43A HIS* 3.9 27.3 + - + +
74A ALA* 1.3 79.7 - - - +
76A GLY* 1.3 58.2 + - - +
77A SER* 3.3 9.6 + - - +
81A GLN 3.8 6.3 - - - +
82A LEU* 5.0 0.2 - - - -
83A GLN* 4.6 4.3 + - - -
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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