Contacts of the helix formed by residues 102 - 113 (chain B) in PDB entry 5A15
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 GLU 102 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81B LEU* 3.4 10.6 - - + +
100B PHE* 3.2 28.6 - - + -
101B PRO* 1.3 96.0 - - + +
103B LYS* 1.3 60.5 + - - +
104B GLY 3.3 2.9 - - - +
105B ARG* 3.2 31.5 + - + +
106B LEU* 3.1 20.3 + - - +
83C ARG* 2.8 44.8 + - - -
84C TYR* 4.3 0.3 + - - -
97C PRO* 4.1 13.1 - - + +
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Residues in contact with LYS 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B LEU* 3.9 26.6 - - + +
100B PHE* 3.7 16.0 - - + +
101B PRO 3.7 2.4 - - - -
102B GLU* 1.3 76.0 - - - +
104B GLY* 1.3 63.7 + - - +
106B LEU* 3.4 4.6 + - - +
107B LYS* 3.1 21.8 + - - +
121B LEU 5.1 3.3 + - - -
122B LEU* 4.1 36.9 - - + +
124B PRO* 6.2 3.2 - - - +
98C ASP* 4.2 6.1 + - - +
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Residues in contact with GLY 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B GLU* 3.3 1.0 - - - +
103B LYS* 1.3 78.7 - - - +
105B ARG* 1.3 60.2 - - - +
107B LYS* 3.4 11.2 - - - +
108B ARG* 3.3 17.0 + - - +
95C VAL* 3.7 19.8 - - - +
96C LEU 5.9 0.2 - - - -
98C ASP* 5.2 5.8 + - - -
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Residues in contact with ARG 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B ASP* 3.7 21.0 + - - +
81B LEU* 3.7 14.8 - - + +
102B GLU* 3.2 38.1 + - + +
103B LYS 3.3 0.4 - - - -
104B GLY* 1.3 75.4 - - - +
106B LEU* 1.3 64.5 + - - +
108B ARG* 3.1 6.5 + - - +
109B GLU* 3.1 26.0 + - - +
83C ARG* 3.8 9.7 - - - +
84C TYR* 3.8 17.6 - - - -
87C ASP* 2.6 34.6 + - - +
94C VAL* 4.6 2.4 - - - +
95C VAL* 2.5 64.7 + - + +
96C LEU 4.1 3.1 + - - +
97C PRO* 3.9 18.8 - - - -
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Residues in contact with LEU 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B LEU* 3.5 39.6 - - + +
84B TYR* 3.8 26.5 - - + -
85B ILE* 4.0 17.3 - - + +
94B VAL* 5.3 3.6 - - + -
96B LEU* 4.4 14.1 - - + -
100B PHE* 4.5 8.1 - - + -
102B GLU 3.1 18.1 + - - +
103B LYS 3.8 5.4 - - - +
104B GLY 3.4 0.2 - - - -
105B ARG* 1.3 77.1 - - - +
107B LYS* 1.3 57.7 + - - +
109B GLU* 3.2 6.1 + - + +
110B ALA* 2.9 27.0 + - - +
118B LEU* 5.4 2.0 - - + -
122B LEU* 3.7 28.9 - - + -
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Residues in contact with LYS 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B LYS 3.1 13.1 + - - +
104B GLY* 3.4 13.5 - - - +
105B ARG 3.2 0.2 - - - -
106B LEU* 1.3 78.1 - - - +
108B ARG* 1.3 61.3 + - - +
110B ALA* 3.3 4.1 + - - +
111B GLU* 3.0 44.6 + - - +
119B VAL* 4.1 15.7 - - + +
122B LEU* 3.8 27.7 - - + +
123B THR* 3.8 30.1 + - - +
124B PRO* 5.6 3.2 - - + +
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Residues in contact with ARG 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B ARG* 3.9 5.3 - - - +
104B GLY 3.3 9.1 + - - +
105B ARG* 3.1 11.7 + - - +
107B LYS* 1.3 76.9 - - - +
109B GLU* 1.3 67.7 + - - +
111B GLU* 3.3 39.7 + - - +
112B TYR* 3.0 41.6 + - - +
91C ASP* 3.1 44.0 + - - +
93C GLN* 4.5 25.5 - - + +
95C VAL* 4.2 20.0 - - + -
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Residues in contact with GLU 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B ARG* 2.9 51.4 + - - +
78B ASP* 4.2 19.8 + - - +
81B LEU* 3.7 26.7 - - + +
85B ILE* 4.2 15.7 - - + -
105B ARG* 3.1 15.3 + - - +
106B LEU* 3.2 8.5 + - + +
108B ARG* 1.3 78.0 - - - +
110B ALA* 1.3 63.2 + - - +
112B TYR* 3.1 2.1 + - - +
113B PHE* 3.0 37.8 + - + -
87C ASP* 4.5 8.1 - - - +
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Residues in contact with ALA 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B ILE* 3.8 8.7 - - - +
106B LEU 2.9 13.8 + - - +
107B LYS* 3.3 12.3 + - - +
109B GLU* 1.3 76.2 - - - +
111B GLU* 1.3 61.2 + - - +
113B PHE 3.5 1.2 + - - -
114B GLN 3.1 4.2 + - - -
115B LEU* 3.0 31.6 + - + +
118B LEU* 3.7 32.3 - - + -
119B VAL* 3.8 17.5 - - + +
122B LEU* 4.3 0.7 - - + -
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Residues in contact with GLU 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B LYS* 3.0 43.5 + - - +
108B ARG* 3.5 35.2 + - - +
109B GLU 3.2 0.2 - - - -
110B ALA* 1.3 75.0 - - - +
112B TYR* 1.3 64.9 + - - +
114B GLN* 3.0 18.7 + - - +
115B LEU 5.1 0.2 - - - +
119B VAL* 3.7 20.5 - - + +
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Residues in contact with TYR 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B LEU* 3.4 37.5 - - + +
75B ILE* 5.1 4.1 - - + +
76B ASP* 5.1 4.5 + - - +
77B ARG* 3.4 69.0 - - + +
108B ARG* 3.0 25.2 + - - +
109B GLU 3.1 6.9 + - - +
111B GLU* 1.3 77.7 - - - +
113B PHE* 1.3 71.0 + + - +
114B GLN* 3.2 12.8 + - - +
91C ASP* 4.7 0.7 - - - -
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Residues in contact with PHE 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B SER* 3.9 1.4 - - - -
50B LEU* 2.9 33.8 + - + -
51B LEU* 4.1 26.9 + - + -
54B MET* 6.3 0.2 - - - -
75B ILE* 4.0 24.5 - - + -
77B ARG* 4.2 9.4 - - + -
82B PHE* 3.4 40.8 - + + -
85B ILE* 4.0 20.6 - - + -
109B GLU* 3.0 45.9 + - + +
112B TYR* 1.3 84.4 - + - +
114B GLN* 1.3 68.2 + - - +
115B LEU* 3.9 21.7 - - + +
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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
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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