Contacts of the helix formed by residues 85 - 108 (chain Z) in PDB entry 5V04
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 85 (chain Z).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B C 5.9 0.8 + - - -
81Z THR* 4.2 3.6 - - + -
82Z LEU* 2.9 11.1 + - + +
84Z SER* 1.3 81.7 - - - +
86Z LYS* 1.3 59.3 + - - +
87Z GLU 3.1 3.6 - - - -
88Z VAL* 2.9 16.1 + - + -
89Z GLU* 2.8 59.6 + - + +
92Z ARG* 4.4 10.5 - - - +
150Z GLU* 3.2 30.4 + - - +
225Z ASP* 3.0 54.4 + - + +
226Z TYR* 4.0 11.4 - - + -
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Residues in contact with LYS 86 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81Z THR* 3.9 16.2 - - + +
82Z LEU 3.1 10.4 + - - +
83Z PRO* 3.3 23.5 + - + +
85Z LYS* 1.3 77.5 - - - +
87Z GLU* 1.3 62.5 - - + +
89Z GLU* 4.4 1.7 - - - +
90Z ARG* 3.7 18.6 + - - +
93Z ARG* 5.6 0.9 + - - -
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Residues in contact with GLU 87 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83Z PRO 4.8 1.0 + - - +
84Z SER 5.3 1.5 + - - +
85Z LYS 3.1 0.6 - - - -
86Z LYS* 1.3 79.2 - - + +
88Z VAL* 1.3 57.0 + - + +
90Z ARG* 2.9 31.9 + - - +
91Z SER* 2.6 41.1 + - - +
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Residues in contact with VAL 88 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84Z SER 4.5 5.4 - - - +
85Z LYS* 2.9 28.9 + - + +
87Z GLU* 1.3 78.0 - - + +
89Z GLU* 1.3 54.2 + - - +
91Z SER* 2.9 12.3 + - - -
92Z ARG* 2.8 70.5 + - + +
225Z ASP* 4.9 8.1 - - + +
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Residues in contact with GLU 89 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B T 4.4 5.9 - - - +
81Z THR* 3.7 28.3 - - + +
85Z LYS* 2.8 45.2 + - + +
86Z LYS 4.4 2.2 - - - +
88Z VAL* 1.3 71.0 - - - +
90Z ARG* 1.3 51.2 + - - +
92Z ARG* 2.9 39.7 + - - +
93Z ARG* 2.6 42.0 + - - +
96Z ARG* 4.6 5.1 + - - -
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Residues in contact with ARG 90 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86Z LYS* 3.7 11.1 + - - +
87Z GLU* 2.9 49.8 + - - +
89Z GLU* 1.3 77.6 - - - +
91Z SER* 1.3 66.0 + - - +
93Z ARG* 2.9 43.9 + - - +
94Z GLU* 3.0 47.1 + - + +
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Residues in contact with SER 91 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87Z GLU* 2.6 26.2 + - - +
88Z VAL* 2.9 15.3 + - - -
90Z ARG* 1.3 78.6 + - - +
92Z ARG* 1.3 59.4 + - - +
94Z GLU* 4.2 11.7 + - - +
95Z ARG* 3.4 32.9 + - - +
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Residues in contact with ARG 92 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B T 3.2 53.6 + - - +
2B C 4.8 9.0 + - - -
85Z LYS* 4.4 5.1 - - - +
88Z VAL* 2.8 40.2 + - + +
89Z GLU* 3.0 35.4 + - - +
91Z SER* 1.3 78.7 - - - +
93Z ARG* 1.3 66.0 + - - +
94Z GLU 3.4 0.2 - - - -
95Z ARG* 2.9 25.5 + - - +
96Z ARG* 3.2 14.6 + - - +
225Z ASP* 4.0 22.0 + - - -
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Residues in contact with ARG 93 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86Z LYS 5.6 1.0 + - - -
89Z GLU* 2.6 21.3 + - - +
90Z ARG* 2.9 36.8 + - - +
92Z ARG* 1.3 71.1 - - - +
94Z GLU* 1.3 65.5 + - - +
96Z ARG* 2.9 52.9 + - - +
97Z GLN* 3.3 27.7 + - + +
124Z ASN* 5.8 1.0 - - - +
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Residues in contact with GLU 94 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90Z ARG* 3.0 44.8 + - + +
91Z SER* 4.2 9.4 - - - +
93Z ARG* 1.3 75.8 - - + +
95Z ARG* 1.3 65.0 + - + +
97Z GLN* 2.9 32.6 + - - +
98Z ALA* 3.1 11.1 + - - +
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Residues in contact with ARG 95 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91Z SER* 3.4 26.7 + - - +
92Z ARG* 2.9 16.4 + - - +
94Z GLU* 1.3 76.8 - - + +
96Z ARG* 1.3 64.6 + - + +
98Z ALA* 3.0 19.9 + - - +
99Z ASN* 3.0 19.3 + - - +
121Z ARG 5.4 0.2 - - - -
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Residues in contact with ARG 96 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B T 3.4 34.2 + - + +
89Z GLU* 4.6 4.8 + - - -
92Z ARG* 3.2 6.3 + - - +
93Z ARG* 2.9 52.8 + - - +
95Z ARG* 1.3 77.4 - - + +
97Z GLN* 1.3 63.9 + - + +
99Z ASN* 2.9 5.9 + - - -
100Z LEU* 2.9 18.6 + - - +
121Z ARG 4.3 8.3 - - - +
122Z SER* 3.5 31.7 - - - +
123Z ILE 3.3 26.4 + - - -
124Z ASN* 3.0 34.8 - - + +
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Residues in contact with GLN 97 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93Z ARG* 3.6 35.6 - - + +
94Z GLU* 2.9 21.2 + - - +
96Z ARG* 1.3 76.0 - - + +
98Z ALA* 1.3 59.1 + - - +
100Z LEU* 3.0 15.2 + - + +
101Z LEU* 2.8 38.6 + - + +
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Residues in contact with ALA 98 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94Z GLU 3.1 7.5 + - - +
95Z ARG* 3.0 15.6 + - - +
97Z GLN* 1.3 75.6 - - - +
99Z ASN* 1.3 58.9 + - - +
100Z LEU 2.9 1.7 + - - -
101Z LEU* 3.0 7.9 + - - +
102Z LYS* 2.6 40.0 + - + +
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Residues in contact with ASN 99 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95Z ARG* 3.0 12.2 + - - +
96Z ARG 2.9 9.4 + - - +
98Z ALA* 1.3 77.7 - - - +
100Z LEU* 1.3 57.5 + - - +
102Z LYS* 4.5 12.8 - - - +
103Z GLY* 3.3 19.1 + - - -
117Z GLU 4.7 0.2 + - - -
118Z CYS* 3.3 34.9 + - - +
119Z PHE* 4.4 2.1 + - - -
121Z ARG* 3.1 38.3 + - - +
122Z SER* 3.7 10.0 + - - -
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Residues in contact with LEU 100 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47Z ALA* 3.7 43.5 - - + +
48Z LYS* 5.8 0.7 - - + -
96Z ARG 2.9 10.2 + - - +
97Z GLN* 3.1 13.7 - - + +
98Z ALA 2.9 0.2 - - - -
99Z ASN* 1.3 76.2 - - - +
101Z LEU* 1.3 74.6 + - + +
103Z GLY 2.9 11.1 + - - -
104Z LYS* 3.0 42.4 + - + +
119Z PHE* 4.3 7.6 - - + -
122Z SER* 4.6 6.1 - - - -
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Residues in contact with LEU 101 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97Z GLN* 2.8 28.1 + - + +
98Z ALA* 3.8 6.1 - - - +
100Z LEU* 1.3 82.3 - - + +
102Z LYS* 1.3 62.1 + - - +
104Z LYS* 3.4 22.1 - - + +
105Z GLN* 3.2 33.4 + - - +
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Residues in contact with LYS 102 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98Z ALA* 2.6 23.0 + - + +
99Z ASN* 4.5 9.0 - - - +
101Z LEU* 1.3 71.7 - - - +
103Z GLY* 1.3 52.8 + - - +
105Z GLN* 2.9 10.8 + - + +
106Z LEU* 2.7 44.3 + - + +
118Z CYS* 4.6 19.6 - - - -
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Residues in contact with GLY 103 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99Z ASN 3.3 15.8 + - - -
100Z LEU 2.9 6.9 + - - -
102Z LYS* 1.3 77.1 - - - +
104Z LYS* 1.3 57.2 + - - +
106Z LEU* 2.9 21.7 + - - +
107Z LEU* 3.2 8.3 + - - +
115Z ALA* 4.0 0.5 - - - +
118Z CYS* 3.7 21.0 - - - +
119Z PHE* 3.5 18.4 - - - -
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Residues in contact with LYS 104 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47Z ALA 5.4 1.2 + - - -
48Z LYS* 3.5 37.1 - - - +
100Z LEU* 3.0 43.9 + - + +
101Z LEU* 3.4 25.7 - - + +
103Z GLY* 1.3 74.4 - - - +
105Z GLN* 1.3 65.0 + - + +
107Z LEU* 2.9 26.2 + - - +
108Z ARG* 3.3 17.8 + - - +
119Z PHE* 3.3 16.0 - - + -
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Residues in contact with GLN 105 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101Z LEU* 3.2 23.4 + - - +
102Z LYS* 2.9 12.6 + - - +
104Z LYS* 1.3 81.9 - - + +
106Z LEU* 1.3 57.9 + - - +
107Z LEU 3.1 0.2 - - - -
108Z ARG* 2.9 41.2 + - - +
109Z GLU* 3.4 12.2 + - - +
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Residues in contact with LEU 106 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102Z LYS* 2.7 23.3 + - + +
103Z GLY* 2.9 13.6 + - - +
105Z GLN* 1.3 76.0 - - - +
107Z LEU* 1.3 59.7 + - - +
109Z GLU* 3.6 25.6 + - + +
111Z LYS* 3.0 50.1 + - + +
114Z GLU* 3.5 45.8 - - + +
115Z ALA* 3.6 3.1 - - + +
118Z CYS* 3.6 16.6 - - - -
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Residues in contact with LEU 107 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48Z LYS* 5.2 8.5 - - - -
103Z GLY 3.2 10.8 + - - +
104Z LYS* 2.9 13.9 + - - +
106Z LEU* 1.3 75.7 - - - +
108Z ARG* 1.3 57.8 + - + +
109Z GLU 3.2 5.9 + - - -
110Z GLY* 3.5 11.8 + - - +
111Z LYS 4.6 0.7 - - - -
112Z VAL* 3.7 31.4 - - + -
115Z ALA* 3.7 20.0 - - + -
119Z PHE* 3.6 27.1 - - + -
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Residues in contact with ARG 108 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48Z LYS* 5.8 4.0 - - - +
104Z LYS* 3.5 19.5 + - - +
105Z GLN* 2.9 27.3 + - + +
107Z LEU* 1.3 78.5 - - - +
109Z GLU* 1.3 61.7 + - + +
110Z GLY 3.4 0.7 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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