Contacts of the helix formed by residues 78 - 92 (chain H) in PDB entry 3LUE
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 ASN 78 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62H ARG* 4.4 16.0 - - - +
69H TYR* 2.7 43.1 + - - +
70H PRO* 3.6 14.5 + - + +
76H VAL* 3.5 10.3 - - - +
77H THR* 1.3 83.2 + - - +
79H TRP* 1.3 60.7 + - - +
80H ASP* 3.9 4.5 + - - +
81H ASP* 3.0 8.3 + - - +
82H MET* 3.1 19.9 + - - +
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Residues in contact with TRP 79 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76H VAL* 3.7 43.1 + - + -
77H THR 4.9 4.7 - - - -
78H ASN* 1.3 73.1 - - - +
80H ASP* 1.3 63.8 + - - +
82H MET* 3.6 5.0 + - + +
83H GLU* 3.0 29.3 + - - +
86H TRP* 4.1 20.2 - + - -
115H ASN* 4.1 34.0 - - + +
118H LYS* 3.4 48.9 - - + +
119H MET* 4.2 13.2 - - + -
122H ILE* 3.5 29.2 - - + -
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Residues in contact with ASP 80 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67H LEU 4.4 11.4 - - - +
68H LYS* 5.2 0.9 - - - -
69H TYR* 1.3 67.6 - - + +
78H ASN* 3.6 4.6 + - - -
79H TRP* 1.3 78.0 - - - +
81H ASP 1.3 46.7 - - - +
83H GLU* 4.0 12.9 - - + +
84H LYS* 5.0 0.2 - - - -
118H LYS* 5.8 0.3 + - - -
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Residues in contact with ASP 81 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34H ILE* 1.7 50.9 - - + +
62H ARG* 4.8 0.2 + - - -
67H LEU* 3.2 31.4 - - - +
69H TYR* 0.4 440.1 + - + +
78H ASN* 2.9 9.8 + - - +
80H ASP* 1.3 65.5 - - - +
82H MET* 1.3 52.1 + - - +
84H LYS* 3.4 0.2 - - - +
85H ILE* 3.1 15.6 + - - +
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Residues in contact with MET 82 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H ASN* 3.2 27.6 - - - +
17H CYS* 4.7 0.4 - - - -
69H TYR* 2.3 2.0 - - - -
70H PRO* 3.8 7.7 - - + +
71H ILE* 3.4 37.7 - - + -
76H VAL* 3.5 23.8 - - + -
78H ASN 3.1 19.9 + - - +
79H TRP* 3.9 7.6 - - + +
81H ASP* 1.3 73.3 - - - +
83H GLU* 1.3 64.0 + - - +
85H ILE* 2.8 42.5 + - + +
86H TRP* 3.1 50.1 + - + +
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Residues in contact with GLU 83 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69H TYR* 2.8 20.9 - - + +
79H TRP 3.0 20.3 + - - +
80H ASP* 3.3 11.1 - - + +
82H MET* 1.3 73.9 - - - +
84H LYS* 1.3 64.1 + - - +
86H TRP* 3.3 10.3 + - - +
87H HIS* 3.1 21.1 + - - +
118H LYS* 4.5 6.2 + - - -
122H ILE* 3.9 36.8 - - + +
126H THR* 3.9 22.7 + - - +
127H PHE* 4.0 6.7 - - + -
120S LYS* 5.3 8.5 - - - +
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Residues in contact with LYS 84 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34H ILE* 2.7 26.0 - - + +
35H VAL* 2.6 20.2 + - - +
67H LEU 2.9 5.2 - - - -
68H LYS* 0.4 254.6 + - + +
69H TYR* 0.8 211.7 - - + +
81H ASP 3.4 0.2 - - - +
83H GLU* 1.3 65.3 - - - +
85H ILE* 1.3 62.9 + - - +
86H TRP 3.2 0.2 + - - -
87H HIS 3.3 0.7 + - - -
88H HIS* 3.0 19.9 + - - +
122S VAL* 3.4 14.4 - - + +
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Residues in contact with ILE 85 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H CYS* 3.9 16.4 - - - -
31H PHE* 4.0 13.9 - - + -
32H PRO 5.1 1.8 - - - +
33H SER* 4.2 30.7 - - - +
34H ILE* 5.1 12.1 - - + +
69H TYR* 4.8 0.7 - - + -
70H PRO* 3.6 26.9 - - + -
71H ILE* 5.0 0.2 - - + -
81H ASP 3.1 9.6 + - - +
82H MET* 2.8 34.1 + - + +
84H LYS* 1.3 74.7 - - - +
86H TRP* 1.3 61.9 + - + +
88H HIS* 3.2 9.3 + - - +
89H THR* 2.8 31.6 + - - +
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Residues in contact with TRP 86 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10H VAL* 3.7 20.1 - - + +
12H ASN* 2.9 38.6 + - - -
17H CYS* 6.2 0.2 - - - -
76H VAL* 5.6 1.6 - - + -
79H TRP* 4.1 16.8 - + - -
82H MET* 3.1 48.2 + - + +
83H GLU* 3.8 7.2 - - - +
85H ILE* 1.3 77.9 - - + +
87H HIS* 1.3 62.9 + - - +
89H THR* 2.8 28.4 + - - -
90H PHE* 3.1 14.7 + + + -
105H LEU* 4.4 11.9 - - + +
119H MET* 4.2 27.8 - - + -
122H ILE* 4.1 20.6 - - + -
123H MET* 3.5 28.7 - - + -
127H PHE* 3.9 12.3 - + + -
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Residues in contact with HIS 87 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69H TYR 4.6 2.7 - - - +
83H GLU 3.1 12.6 + - - +
84H LYS* 3.4 9.2 - - - +
86H TRP* 1.3 72.4 - - - +
88H HIS* 1.3 58.2 + - - +
90H PHE* 4.5 0.9 - - - -
91H TYR* 2.9 75.9 + + + +
92H ASN* 5.4 2.2 - - - -
127H PHE* 3.7 18.0 - - + -
118S GLY 5.6 1.6 - - - -
119S VAL* 4.4 8.7 - - + -
120S LYS* 4.0 45.5 + - + +
122S VAL* 4.2 8.7 - - + -
143S THR* 4.1 18.4 - - + +
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Residues in contact with HIS 88 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31H PHE* 4.2 22.7 - + - +
84H LYS 3.0 12.7 + - - +
85H ILE* 3.3 10.3 - - - +
87H HIS* 1.3 73.0 - - - +
89H THR* 1.3 58.0 + - - +
92H ASN* 3.0 44.4 + - + +
93H GLU* 2.7 64.9 + - - +
122S VAL* 4.3 18.3 + - + +
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Residues in contact with THR 89 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10H VAL* 3.9 22.5 - - + +
17H CYS* 5.7 0.2 - - - -
19H ALA* 3.7 31.0 - - + -
31H PHE* 3.5 17.2 - - + -
85H ILE* 2.8 18.3 + - - +
86H TRP* 2.8 26.7 + - - -
88H HIS* 1.3 72.2 - - - +
90H PHE* 1.3 58.9 + - + +
93H GLU* 3.3 8.6 + - - +
94H LEU* 2.7 42.0 + - + +
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Residues in contact with PHE 90 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H LEU* 3.3 34.3 - - + -
10H VAL* 4.5 17.0 - - + -
86H TRP* 3.1 30.9 + + + -
87H HIS* 4.1 1.8 - - - +
89H THR* 1.3 78.3 - - + +
91H TYR* 1.3 61.4 + - + +
94H LEU* 4.8 0.7 - - + -
95H ARG 2.8 31.0 + - - -
96H VAL* 2.8 23.0 + - + +
98H PRO* 3.6 32.5 - - + -
103H VAL* 4.0 17.5 - - + -
105H LEU* 5.6 0.4 - - + -
123H MET* 4.0 30.1 - - + -
127H PHE* 4.2 18.8 - + - -
142S TRP* 3.6 0.9 - - - -
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Residues in contact with TYR 91 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87H HIS* 2.9 71.1 + + + +
90H PHE* 1.3 65.3 - - + +
92H ASN* 1.3 64.7 + - - +
96H VAL 4.0 0.4 - - - -
98H PRO* 3.7 23.9 - - + +
99H GLU* 4.8 3.6 + - - -
127H PHE* 4.1 20.9 + + - -
142S TRP* 1.2 58.3 - - + +
143S THR* 4.5 6.3 - - + +
146S LEU* 1.0 129.8 - - + +
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Residues in contact with ASN 92 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87H HIS* 5.4 2.1 - - - -
88H HIS* 3.0 43.6 + - + +
90H PHE 3.4 0.2 - - - -
91H TYR* 1.3 94.9 + - - +
93H GLU* 1.3 71.2 + - - +
94H LEU 3.9 0.2 - - - -
95H ARG* 3.5 18.7 - - - +
43S TRP* 4.6 4.5 - - - -
47S GLN* 4.3 4.5 + - - +
122S VAL* 5.0 5.9 - - - +
124S ILE* 4.2 14.4 - - - +
139S GLY* 2.7 44.7 + - - -
142S TRP* 3.7 0.7 - - - -
143S THR* 3.3 9.8 + - - -
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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