Contacts of the helix formed by residues 58 - 72 (chain A) in PDB entry 4KPD
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 58 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A LYS* 3.8 20.9 - - + -
17A PHE* 3.9 20.6 - + + -
18A VAL* 3.5 26.1 - - + +
53A ALA 3.6 20.4 - - - -
54A ILE* 3.5 16.3 - - + +
55A GLY* 2.9 23.9 + - - -
56A GLY* 3.2 28.8 - - - -
57A LYS* 1.4 78.1 - - - +
59A ASN* 1.4 57.6 + - - +
60A ARG 3.3 2.2 - - - -
61A GLY 3.5 0.3 + - - -
62A LEU* 2.9 35.3 + - + +
90A TRP* 3.8 21.3 - + - -
93A GLU* 3.3 27.2 + - - -
404A IPE 4.4 3.2 + - - -
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Residues in contact with ASN 59 (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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10A TYR* 3.7 4.7 - - + -
57A LYS* 3.2 36.3 - - + +
58A TYR* 1.4 76.4 - - - +
60A ARG* 1.3 59.3 + - + +
62A LEU* 4.6 3.4 - - - -
63A THR* 2.6 37.7 + - - -
93A GLU* 4.0 0.2 + - - -
239A PHE* 4.7 5.2 - - + -
344A LEU* 4.8 10.8 - - + -
347A LYS* 2.9 45.8 + - - +
348A ILE* 4.2 21.5 - - - +
351A ARG* 5.4 1.0 - - - +
404A IPE 4.9 7.8 + - - +
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Residues in contact with ARG 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A TYR 3.3 0.6 - - - -
59A ASN* 1.3 78.9 - - + +
61A GLY* 1.3 65.1 + - - +
63A THR* 3.3 11.9 + - - -
64A VAL* 3.3 11.8 + - - +
92A VAL* 3.6 27.8 - - + -
93A GLU* 3.6 8.7 + - - +
96A GLN* 3.1 30.4 - - - +
204A PHE* 3.5 15.8 - - - -
205A SER* 2.7 56.0 + - - +
209A PRO* 3.4 17.2 - - + +
239A PHE* 4.0 6.4 - - - -
404A IPE 2.8 59.6 + - - +
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Residues in contact with GLY 61 (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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17A PHE* 3.6 19.5 - - - -
60A ARG* 1.3 74.5 - - - +
62A LEU* 1.3 61.8 + - - +
64A VAL* 3.3 8.0 + - - +
65A VAL* 3.2 19.4 + - - +
89A GLY* 3.2 32.1 + - - -
93A GLU* 2.9 14.0 + - - -
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Residues in contact with LEU 62 (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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10A TYR* 3.6 40.2 - - + +
13A GLU* 3.6 42.6 - - + +
14A LYS* 4.2 13.0 - - + -
17A PHE* 3.7 18.8 - - + -
57A LYS 4.0 14.6 - - - +
58A TYR* 2.9 30.2 + - + +
59A ASN* 4.8 0.9 - - - +
61A GLY* 1.3 72.4 - - - +
63A THR* 1.3 57.1 + - - +
65A VAL* 3.7 6.0 - - + +
66A VAL* 2.8 38.8 + - + +
347A LYS* 5.6 2.0 - - - -
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Residues in contact with THR 63 (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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10A TYR* 2.7 25.7 + - - +
59A ASN 2.6 25.5 + - - -
60A ARG 3.3 7.1 + - - -
62A LEU* 1.3 76.1 - - - +
64A VAL* 1.4 55.0 + - - +
66A VAL* 4.9 0.7 - - - -
67A ALA* 2.8 35.9 + - - +
209A PRO* 3.6 19.5 - - + -
210A ILE* 3.4 31.9 - - + -
344A LEU* 3.6 21.9 - - + +
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Residues in contact with VAL 64 (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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60A ARG 3.3 14.2 + - - +
61A GLY 3.3 7.0 + - - +
63A THR* 1.4 75.1 - - - +
65A VAL* 1.3 57.3 + - - +
68A PHE* 2.9 29.9 + - + +
85A ALA* 3.5 23.3 - - + +
88A VAL* 3.9 16.2 - - + +
89A GLY* 3.7 18.2 - - - +
92A VAL* 3.9 11.9 - - + -
209A PRO* 3.6 32.1 - - + +
212A ALA* 4.7 0.9 - - + -
213A ALA* 3.8 10.6 - - + +
216A MET* 4.7 7.2 - - - -
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Residues in contact with VAL 65 (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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13A GLU* 3.5 35.9 - - + +
17A PHE* 3.9 13.2 - - + -
61A GLY 3.2 13.6 + - - +
62A LEU* 3.2 10.0 + - + +
64A VAL* 1.3 76.8 - - - +
66A VAL* 1.3 62.6 + - + +
68A PHE* 3.4 4.6 + - - +
69A ARG* 3.2 29.7 + - + +
82A LEU* 6.6 0.2 - - + -
85A ALA* 4.2 6.5 - - + +
86A TRP* 3.6 44.9 - - + +
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Residues in contact with VAL 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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9A VAL* 3.7 54.1 - - + +
10A TYR* 4.6 20.6 - - + +
13A GLU* 4.4 16.2 - - + -
62A LEU* 2.8 26.8 + - + +
63A THR 4.3 1.1 - - - +
65A VAL* 1.3 71.7 - - - +
67A ALA* 1.4 61.1 + - - +
69A ARG* 3.3 8.4 + - - +
70A GLU* 3.2 41.5 + - + +
339A ALA 6.0 0.2 - - - +
343A GLY* 6.4 0.7 - - - -
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Residues in contact with ALA 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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63A THR 2.8 25.0 + - - +
66A VAL* 1.4 71.3 - - - +
68A PHE* 1.4 58.0 + - - +
70A GLU* 3.2 11.3 + - - +
71A LEU* 2.9 39.6 + - + +
210A ILE* 3.9 23.8 - - + -
213A ALA* 3.7 18.2 - - + -
340A VAL* 4.5 6.7 - - + +
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Residues in contact with PHE 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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64A VAL* 2.9 20.7 + - + +
65A VAL 3.8 4.3 - - - +
66A VAL 3.4 0.2 - - - -
67A ALA* 1.4 74.4 - - - +
69A ARG* 1.3 61.3 + - + +
71A LEU* 4.8 2.2 - - - -
72A VAL* 3.0 60.1 + - + +
77A GLN* 4.3 15.9 - - + -
81A SER* 3.7 41.5 - - - -
82A LEU* 4.5 11.2 - - + -
85A ALA* 3.6 21.8 - - + -
152A TYR* 5.8 0.9 - - - -
213A ALA* 3.7 13.5 - - + +
216A MET* 3.8 43.5 - - + -
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Residues in contact with ARG 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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9A VAL* 6.5 0.4 - - - -
13A GLU* 2.7 32.4 + - - -
65A VAL* 3.2 21.5 + - + +
66A VAL* 3.3 10.9 + - + +
68A PHE* 1.3 77.2 - - + +
70A GLU* 1.3 61.5 + - + +
72A VAL 3.5 3.3 - - - +
74A PRO* 5.8 0.7 - - - +
77A GLN* 3.0 44.5 + - - +
82A LEU* 3.8 33.3 - - + +
86A TRP* 6.3 0.8 - - - -
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Residues in contact with GLU 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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9A VAL* 4.9 7.8 - - + +
66A VAL* 3.2 35.7 + - + +
67A ALA* 3.2 6.2 + - - +
69A ARG* 1.3 78.5 - - + +
71A LEU* 1.3 60.3 + - - +
72A VAL 3.7 1.1 - - - -
337A PRO* 3.8 20.4 - - + +
339A ALA* 4.0 19.8 - - + +
340A VAL* 3.3 40.4 - - + +
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Residues in contact with LEU 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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67A ALA* 2.9 25.9 + - + +
68A PHE* 4.2 2.0 - - - +
70A GLU* 1.3 78.0 - - - +
72A VAL* 1.3 61.3 + - - +
73A GLU 4.1 1.0 + - - -
210A ILE* 4.9 1.1 - - + +
213A ALA* 4.1 7.4 - - + -
214A MET* 4.0 39.0 - - + +
217A ALA* 3.9 18.3 - - + +
219A ILE* 4.0 16.6 - - + +
336A LEU* 3.8 28.3 - - + -
337A PRO* 4.0 17.9 - - + -
340A VAL* 4.4 11.4 - - + -
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Residues in contact with VAL 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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68A PHE* 3.0 46.2 + - + +
69A ARG 3.5 4.5 - - - +
70A GLU 4.8 0.5 - - - -
71A LEU* 1.3 76.5 + - - +
73A GLU* 1.3 70.9 + - - +
74A PRO* 3.4 3.3 - - - +
76A LYS* 3.8 23.3 - - + +
77A GLN* 2.7 40.8 + - + -
81A SER* 5.6 0.2 - - - +
216A MET 4.9 0.4 - - - +
217A ALA* 3.7 24.9 - - + -
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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