Contacts of the helix formed by residues 74 - 88 (chain A) in PDB entry 1PJK
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 LYS 74 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A VAL* 1.3 91.4 + - + +
75A LYS* 1.3 69.3 + - - +
76A LYS* 3.0 24.9 - - + +
77A LYS* 3.0 24.5 + - + +
78A ILE* 3.2 17.3 + - - +
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Residues in contact with LYS 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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74A LYS* 1.3 77.0 - - - +
76A LYS* 1.3 60.4 + - - +
78A ILE* 3.9 9.4 - - + -
79A LYS* 3.0 68.7 + - + +
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Residues in contact with LYS 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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26A TYR* 3.5 39.8 - - + -
27A GLU* 4.6 20.1 + - + +
74A LYS* 4.1 21.8 - - + +
75A LYS* 1.3 79.9 - - - +
77A LYS* 1.3 62.2 + - - +
79A LYS* 4.2 2.1 - - - +
80A ARG* 3.2 29.3 + - - +
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Residues in contact with LYS 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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50A TYR* 3.9 49.4 - - + -
73A VAL* 5.2 9.0 - - + -
74A LYS* 3.0 18.3 + - + +
76A LYS* 1.3 78.8 - - - +
78A ILE* 1.3 69.9 + - + +
80A ARG* 3.5 24.4 - - - +
81A GLU* 3.2 24.3 + - - +
177A GLY* 3.6 22.4 + - - +
178A LEU* 3.5 30.5 - - - +
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Residues in contact with ILE 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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50A TYR 5.8 0.4 - - - +
70A LEU* 3.5 41.1 - - + +
71A LYS 4.2 12.6 - - - +
72A PRO* 5.8 0.9 - - + -
73A VAL* 5.3 4.5 - - + +
74A LYS 3.2 23.3 + - - +
75A LYS* 3.9 9.6 - - + +
76A LYS 3.3 0.2 - - - -
77A LYS* 1.3 83.2 - - + +
79A LYS* 1.3 68.5 + - + +
81A GLU* 3.5 5.1 + - - +
82A ILE* 3.3 30.2 + - + +
109A PRO* 3.5 30.1 - - + -
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Residues in contact with LYS 79 (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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26A TYR* 3.4 22.9 - - + +
27A GLU* 3.4 19.4 + - - +
29A HIS* 3.4 29.9 + - + +
31A VAL* 4.8 16.4 - - + -
75A LYS* 3.0 61.0 + - + +
76A LYS* 4.2 2.7 - - - +
78A ILE* 1.3 78.5 - - + +
80A ARG* 1.3 60.2 + - - +
82A ILE* 3.4 8.5 + - + +
83A LYS* 2.9 32.6 + - - +
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Residues in contact with ARG 80 (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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26A TYR* 3.6 39.6 + - + -
76A LYS* 3.2 22.7 + - - +
77A LYS* 3.5 26.5 - - - +
78A ILE 3.2 0.2 - - - -
79A LYS* 1.3 76.4 - - - +
81A GLU* 1.3 65.2 + - - +
83A LYS* 3.4 1.4 + - - +
84A ILE* 3.1 39.1 + - + +
155A ARG* 4.0 6.2 - - - +
176A TRP 5.4 0.2 - - - -
177A GLY 3.2 24.0 + - - -
178A LEU* 4.1 7.9 - - - +
179A ALA 3.0 24.8 + - - -
180A GLU* 3.5 25.9 + - - +
341A CL 3.3 27.9 - - - +
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Residues in contact with GLU 81 (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 LYS* 2.8 30.5 + - - -
70A LEU* 4.0 18.5 - - + +
77A LYS* 3.2 17.0 + - - +
78A ILE* 4.0 5.7 - - - +
79A LYS 3.4 0.4 - - - -
80A ARG* 1.3 78.7 - - - +
82A ILE* 1.3 63.4 + - - +
84A ILE* 4.1 1.8 - - - +
85A LEU* 3.2 45.0 + - + +
111A LEU* 3.8 16.8 - - + +
113A PHE* 4.7 2.4 - - - -
175A ASP* 4.7 0.2 - - - -
176A TRP 3.8 25.7 + - - +
177A GLY* 3.7 24.4 + - - +
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Residues in contact with ILE 82 (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 HIS* 4.2 16.4 - - + +
31A VAL* 4.4 21.3 - - + -
33A TRP* 5.8 0.2 - - + -
78A ILE* 3.3 29.9 + - + +
79A LYS* 3.7 8.1 - - - +
80A ARG 3.3 0.2 - - - -
81A GLU* 1.3 79.2 - - - +
83A LYS* 1.3 57.5 + - - +
85A LEU* 3.6 7.2 + - - +
86A GLU* 3.1 31.9 + - - +
97A LEU* 4.3 2.8 - - + +
100A ILE* 3.9 36.3 - - + -
109A PRO* 4.7 4.9 - - + -
111A LEU* 3.5 33.7 - - + -
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Residues in contact with LYS 83 (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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22A GLU* 3.0 29.1 + - - +
23A TYR* 3.2 24.4 + - - +
25A ASP 5.6 0.9 - - - -
26A TYR* 4.1 18.8 - - + -
29A HIS* 3.6 41.7 - - + +
79A LYS 2.9 18.1 + - - +
80A ARG 4.0 3.1 - - - +
81A GLU 3.3 0.4 - - - -
82A ILE* 1.3 74.7 - - - +
84A ILE* 1.3 60.9 + - - +
86A GLU* 3.9 7.2 - - - +
87A ASN* 2.9 56.9 + - - +
181A PHE* 4.7 4.0 - - + -
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Residues in contact with ILE 84 (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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80A ARG* 3.1 27.1 + - + +
81A GLU* 4.1 3.4 - - - +
83A LYS* 1.3 75.0 - - - +
85A LEU* 1.3 62.4 + - - +
87A ASN* 3.5 4.7 + - - +
88A LEU* 3.0 54.8 + - + +
152A ILE* 4.0 13.7 - - + -
176A TRP* 3.9 23.8 - - + +
179A ALA* 3.5 36.3 - - + +
180A GLU* 4.0 3.8 - - - +
181A PHE* 3.5 35.0 - - + -
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Residues in contact with LEU 85 (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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81A GLU* 3.2 41.3 + - + +
82A ILE* 3.8 5.4 - - - +
83A LYS 3.4 0.2 - - - -
84A ILE* 1.3 76.4 - - - +
86A GLU* 1.3 57.4 + - - +
88A LEU* 3.4 5.3 + - + -
89A ARG* 3.0 28.6 + - - +
94A ILE* 5.4 2.4 - - + +
95A ILE* 4.1 19.3 - - + +
97A LEU* 4.2 21.4 + - + +
111A LEU* 4.2 7.4 - - + -
113A PHE* 3.8 37.7 - - + -
176A TRP* 3.7 34.5 - - + +
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Residues in contact with GLU 86 (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 HIS* 3.6 28.3 + - - -
32A GLU* 5.7 4.5 + - - +
82A ILE* 3.1 24.0 + - + +
83A LYS* 4.0 7.9 - - + +
85A LEU* 1.3 74.0 - - - +
87A ASN* 1.3 66.6 + - - +
89A ARG* 3.3 58.9 + - - +
97A LEU* 4.2 5.4 - - + -
100A ILE* 4.1 14.4 - - - +
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Residues in contact with ASN 87 (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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23A TYR* 3.1 62.2 + - + +
83A LYS* 2.9 41.1 + - - +
84A ILE* 3.7 6.3 - - - +
86A GLU* 1.3 80.0 - - - +
88A LEU* 1.3 59.1 + - - +
89A ARG 3.7 2.3 + - - +
146A TYR* 4.7 3.5 + - - -
150A MET* 3.7 18.2 - - - +
152A ILE* 4.6 4.6 - - + +
181A PHE* 3.7 12.9 - - - -
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Residues in contact with LEU 88 (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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84A ILE* 3.0 38.7 + - + +
85A LEU* 3.7 4.5 - - - +
86A GLU 3.2 0.2 - - - -
87A ASN* 1.3 75.7 - - - +
89A ARG* 1.3 64.8 + - - +
90A GLY 3.3 0.5 + - - -
91A GLY* 3.1 18.5 + - - -
94A ILE* 3.9 24.5 - - + +
146A TYR* 4.0 11.4 - - + -
147A CYS* 3.8 19.3 - - + -
150A MET* 3.8 34.1 - - + -
152A ILE* 4.2 11.4 - - + -
176A TRP* 3.7 32.1 - - + -
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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