Contacts of the helix formed by residues 102 - 113 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81C LEU* 3.5 11.9 - - + +
100C PHE* 3.2 29.5 - - + -
101C PRO* 1.3 96.7 - - + +
103C LYS* 1.3 63.2 + - - +
104C GLY 3.3 3.8 - - - +
105C ARG* 3.2 30.4 + - + +
106C LEU* 3.1 16.1 + - - +
83D ARG* 2.9 43.5 + - - -
84D TYR* 4.5 0.2 + - - -
96D LEU 5.8 0.2 - - - -
97D PRO* 3.8 14.5 - - + +
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Residues in contact with LYS 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C LEU* 3.7 29.8 - - + +
97C PRO 5.7 0.2 + - - -
99C HIS* 5.1 1.8 - - - +
100C PHE* 3.5 36.5 + - + +
101C PRO 3.8 2.4 + - - -
102C GLU* 1.3 74.5 - - - +
104C GLY* 1.3 61.0 + - - +
106C LEU* 3.3 4.7 + - - +
107C LYS* 2.9 29.5 + - - +
122C LEU* 4.4 23.0 - - + +
98D ASP* 4.8 5.1 + - - +
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Residues in contact with GLY 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C GLU* 3.3 1.0 - - - +
103C LYS* 1.3 80.3 - - - +
105C ARG* 1.3 59.6 + - - +
107C LYS* 3.4 11.2 + - - +
108C ARG* 3.2 19.1 + - - +
95D VAL* 3.7 20.5 - - - +
98D ASP* 5.7 1.4 + - - -
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Residues in contact with ARG 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C ASP* 3.7 8.1 + - - +
81C LEU* 3.7 14.3 - - + +
102C GLU* 3.2 38.8 + - + +
103C LYS 3.3 0.6 - - - -
104C GLY* 1.3 74.6 - - - +
106C LEU* 1.3 65.4 + - - +
108C ARG* 2.9 7.5 + - - +
109C GLU* 2.9 26.4 + - - +
83D ARG* 3.4 28.9 - - - +
84D TYR* 3.8 19.4 - - - -
87D ASP* 2.9 30.3 + - - +
94D VAL* 4.4 4.9 - - - +
95D VAL* 2.8 60.5 + - + +
96D LEU 4.0 1.6 - - - +
97D PRO* 3.9 17.0 - - - -
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Residues in contact with LEU 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C LEU* 3.6 37.9 - - + +
84C TYR* 3.8 25.6 - - + -
85C ILE* 4.1 16.8 - - + +
94C VAL* 5.2 2.0 - - + -
96C LEU* 4.2 15.0 - - + -
100C PHE* 4.3 11.0 - - + -
102C GLU 3.1 17.9 + - - +
103C LYS* 3.7 5.4 - - - +
105C ARG* 1.3 76.2 - - - +
107C LYS* 1.3 53.4 + - - +
109C GLU* 3.3 5.7 + - + +
110C ALA* 2.8 32.2 + - - +
118C LEU* 5.4 4.9 - - + -
122C LEU* 3.6 26.5 - - + -
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Residues in contact with LYS 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C LYS 2.9 13.2 + - - +
104C GLY* 3.4 13.8 + - - +
105C ARG 3.1 0.2 - - - -
106C LEU* 1.3 74.9 - - - +
108C ARG* 1.3 60.4 + - - +
110C ALA* 3.4 3.8 - - - +
111C GLU* 2.4 60.5 + - - +
119C VAL* 4.1 18.2 - - + +
122C LEU* 3.7 19.9 - - + +
123C THR* 3.4 35.2 - - - +
124C PRO* 6.1 0.7 - - + -
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Residues in contact with ARG 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C ARG* 4.0 4.8 - - - +
104C GLY 3.2 9.4 + - - +
105C ARG* 2.9 12.8 + - - +
107C LYS* 1.3 79.0 - - - +
109C GLU* 1.3 58.3 + - - +
111C GLU* 3.2 40.6 + - - +
112C TYR* 3.0 42.7 + - - +
91D ASP* 2.9 43.3 + - - +
93D GLN* 4.2 28.8 - - + +
95D VAL* 4.4 15.7 - - + -
117I ASP* 3.5 32.5 + - - -
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Residues in contact with GLU 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C ARG* 2.8 51.7 + - - +
78C ASP* 4.2 21.2 - - - +
81C LEU* 3.8 26.2 - - + +
85C ILE* 4.1 16.6 - - + -
105C ARG* 2.9 18.2 + - - +
106C LEU* 3.5 9.0 - - + +
108C ARG* 1.3 76.5 - - - +
110C ALA* 1.3 63.6 + - - +
112C TYR* 3.2 1.3 + - - +
113C PHE* 3.0 38.3 + - + -
87D ASP* 4.4 8.7 - - - +
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Residues in contact with ALA 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C ILE* 3.9 9.6 - - - +
106C LEU 2.8 16.6 + - - +
107C LYS* 3.1 10.3 + - - +
109C GLU* 1.3 77.7 - - - +
111C GLU* 1.3 60.7 + - - +
113C PHE 3.7 0.5 + - - -
114C GLN 3.2 3.5 + - - -
115C LEU* 3.0 30.8 + - - +
118C LEU* 3.8 31.6 - - + -
119C VAL* 3.6 18.5 - - + +
122C LEU* 4.4 0.4 - - + -
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Residues in contact with GLU 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C LYS* 2.4 54.5 + - - +
108C ARG* 3.2 36.0 + - - +
110C ALA* 1.3 75.4 - - - +
112C TYR* 1.3 65.2 + - - +
114C GLN* 3.1 18.2 + - - +
119C VAL* 3.7 22.3 - - + +
93D GLN* 5.7 0.3 - - - +
117I ASP* 4.8 7.2 - - - +
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Residues in contact with TYR 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C LEU* 3.3 33.8 - - + +
54C MET* 6.0 0.2 - - - -
75C ILE* 5.2 2.8 - - + +
76C ASP* 5.2 5.0 + - - +
77C ARG* 3.5 61.2 - - + +
108C ARG* 3.0 31.2 + - - +
109C GLU 3.2 6.0 + - - +
111C GLU* 1.3 77.9 - - - +
113C PHE* 1.3 76.3 + + - +
114C GLN* 3.2 14.7 + - - +
91D ASP* 4.7 1.3 - - - -
47I PRO* 5.2 10.8 + - + +
48I HIS* 4.2 14.0 + - - -
117I ASP* 5.6 2.5 - - - -
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Residues in contact with PHE 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C SER* 3.7 4.2 - - - -
50C LEU* 3.0 33.0 + - + -
51C LEU* 3.9 36.0 + - + -
54C MET* 5.8 0.7 - - - -
75C ILE* 3.8 17.3 - - + -
77C ARG* 3.7 19.5 - - + -
82C PHE* 3.8 28.5 - + - -
85C ILE* 4.2 17.3 - - + -
109C GLU* 3.0 45.2 + - - +
112C TYR* 1.3 93.3 - + - +
114C GLN* 1.3 67.9 + - - +
115C LEU* 3.9 18.4 - - + +
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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