Contacts of the helix formed by residues 65 - 78 (chain A) in PDB entry 1KTW
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 ASP 65 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A CA 2.5 29.7 - - - -
51A LEU* 5.4 0.2 - - - +
57A ALA* 4.0 11.7 - - + +
58A ASN* 3.2 23.7 + - - +
63A SER 3.2 1.0 - - - +
64A ASP* 1.3 73.6 - - - +
66A SER* 1.3 64.1 + - - +
67A ASN 3.4 2.7 - - - -
68A ALA* 3.4 9.0 + - - +
69A LEU 3.2 17.0 + - - -
92A TYR* 3.4 14.8 - - + -
93A HIS 2.9 30.0 + - - +
94A PHE* 3.6 25.5 - - + -
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Residues in contact with SER 66 (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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64A ASP* 2.7 30.0 + - - -
65A ASP* 1.3 77.6 - - - +
67A ASN* 1.3 62.3 + - - +
69A LEU 3.4 0.3 + - - -
70A GLN* 3.0 26.4 + - - +
93A HIS 3.7 0.8 + - - -
94A PHE* 3.5 5.2 - - - -
95A LEU* 3.2 30.2 + - - +
97A ILE* 3.7 20.6 - - - +
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Residues in contact with ASN 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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64A ASP* 4.6 2.8 + - - -
65A ASP 3.4 0.8 - - - -
66A SER* 1.3 78.6 - - - +
68A ALA* 1.3 63.4 + - - +
70A GLN* 3.4 4.8 + - - +
71A ARG* 2.9 61.1 + - - +
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Residues in contact with ALA 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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51A LEU* 3.7 5.9 - - + +
55A PHE* 3.5 26.4 - - - +
56A GLY 4.6 0.7 - - - -
57A ALA* 4.0 26.9 - - + +
65A ASP* 3.4 11.0 + - - +
66A SER 3.3 0.6 - - - -
67A ASN* 1.3 80.9 + - - +
69A LEU* 1.3 62.6 + - - +
71A ARG* 3.6 13.7 + - - +
72A ALA* 3.1 22.9 + - - +
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Residues in contact with LEU 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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51A LEU* 3.6 12.0 - - + +
65A ASP 3.2 5.4 + - - +
66A SER 3.9 3.4 - - - +
67A ASN 3.3 0.2 - - - -
68A ALA* 1.3 77.2 - - - +
70A GLN* 1.3 64.8 + - - +
72A ALA* 3.2 1.6 + - - +
73A ILE* 3.0 44.0 + - + +
85A LEU* 3.6 27.6 - - + -
87A ILE* 4.7 10.3 - - + -
94A PHE* 3.6 48.0 - - + -
97A ILE* 4.0 21.3 - - + -
99A MET* 4.9 1.8 - - + -
105A ILE* 4.5 8.1 - - + -
127A PHE* 4.2 9.6 - - + -
140A PHE* 5.9 0.7 - - + -
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Residues in contact with GLN 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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66A SER 3.0 17.9 + - - +
67A ASN* 3.9 5.8 - - - +
69A LEU* 1.3 79.1 - - - +
71A ARG* 1.3 56.1 + - + +
73A ILE* 3.5 7.2 + - - +
74A ASN* 3.0 65.6 + - - +
96A GLY 4.5 1.4 - - - +
97A ILE* 3.9 11.7 - - + +
98A GLN* 2.9 56.4 + - - +
100A LYS* 4.1 2.4 - - - +
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Residues in contact with ARG 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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55A PHE* 3.1 57.6 + - + +
67A ASN* 2.9 46.8 + - - +
68A ALA* 4.0 8.3 - - - +
70A GLN* 1.3 74.0 - - + +
72A ALA* 1.3 61.5 + - - +
74A ASN* 3.4 7.5 + - - +
75A ALA* 2.9 32.9 + - - +
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Residues in contact with ALA 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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51A LEU* 4.4 2.7 - - + -
55A PHE* 3.8 30.9 - - + -
68A ALA 3.1 18.4 + - - +
69A LEU* 3.4 7.0 - - - +
71A ARG* 1.3 77.8 - - - +
73A ILE* 1.3 61.8 + - - +
75A ALA* 3.9 1.2 - - - +
76A ILE* 3.1 31.5 + - + +
85A LEU* 3.9 28.5 - - + -
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Residues in contact with ILE 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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69A LEU* 3.0 36.6 + - + +
70A GLN* 3.7 6.3 - - - +
72A ALA* 1.3 76.1 - - - +
74A ASN* 1.3 58.4 + - - +
76A ILE* 3.4 1.9 + - - -
77A SER* 3.0 27.0 + - - -
85A LEU* 4.9 2.2 - - + -
97A ILE* 3.5 33.0 - - + -
98A GLN 3.8 6.1 - - - +
99A MET* 3.6 19.3 - - - -
100A LYS* 3.7 37.7 - - + +
103A VAL* 3.6 28.9 - - + +
105A ILE* 4.5 3.1 - - + -
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Residues in contact with ASN 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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70A GLN* 3.0 39.6 + - - +
71A ARG* 3.9 6.8 - - - +
73A ILE* 1.3 73.9 - - - +
75A ALA* 1.3 65.3 + - - +
77A SER* 3.4 5.6 + - - -
78A ARG* 3.2 59.1 + - - +
100A LYS* 2.9 33.0 + - - +
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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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49A TYR* 4.3 10.8 - - + +
55A PHE* 4.1 19.5 - - + -
71A ARG 2.9 19.2 + - - +
72A ALA 3.9 3.4 - - - +
74A ASN* 1.3 76.0 - - - +
76A ILE* 1.3 65.0 + - - +
78A ARG* 3.5 19.7 + - - +
79A LYS* 3.8 17.0 - - - +
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Residues in contact with ILE 76 (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 VAL* 4.2 6.1 - - + -
49A TYR* 3.5 25.4 - - + -
72A ALA 3.1 20.6 + - - +
73A ILE 3.7 4.3 - - - +
75A ALA* 1.3 78.1 - - - +
77A SER* 1.3 62.2 + - - +
79A LYS* 3.1 24.1 + - - +
82A GLY* 3.6 7.2 - - - -
83A GLY* 3.3 35.0 - - - +
84A THR 3.9 15.3 - - - +
85A LEU* 3.8 31.0 - - + +
102A ASN 3.9 1.3 - - - +
103A VAL* 3.8 20.4 - - + -
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Residues in contact with SER 77 (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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73A ILE 3.0 17.6 + - - -
74A ASN* 3.4 5.4 + - - -
76A ILE* 1.3 76.4 - - - +
78A ARG* 1.3 62.0 + - - +
79A LYS 3.2 8.6 + - - +
82A GLY* 5.2 1.3 - - - -
100A LYS* 3.5 24.0 - - - +
101A SER* 2.8 34.5 + - - +
102A ASN* 5.5 2.9 + - - +
103A VAL* 4.0 1.8 - - - +
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Residues in contact with ARG 78 (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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74A ASN* 3.2 48.2 + - - +
75A ALA* 3.8 11.2 - - - +
76A ILE 3.1 1.4 - - - -
77A SER* 1.3 76.2 - - - +
79A LYS* 1.3 65.2 + - + +
80A PRO* 3.8 4.7 - - - +
100A LYS* 5.9 0.6 - - - +
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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