Contacts of the helix formed by residues 88 - 107 (chain C) in PDB entry 3LOC
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 ALA 88 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86C ASP 3.7 0.6 + - - -
87C PHE* 1.3 70.6 - - - +
89C PRO* 1.4 65.4 - - + +
90C LEU 3.3 1.8 - - - +
91C ALA* 3.3 18.2 + - + +
92C ALA* 2.9 28.2 + - - +
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Residues in contact with PRO 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C PHE 3.3 6.0 - - - +
88C ALA* 1.4 83.5 - - + +
90C LEU* 1.3 59.9 + - + +
92C ALA* 3.3 6.4 + - + +
93C ILE* 2.9 36.0 + - - +
147C TRP* 3.5 55.0 - - + +
152C LYS* 3.9 29.8 - - + +
153C LEU* 4.1 14.6 - - + -
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Residues in contact with LEU 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C ALA* 3.3 0.8 - - - +
89C PRO* 1.3 78.4 - - + +
91C ALA* 1.3 66.8 + - - +
93C ILE* 3.4 0.7 + - - -
94C LYS* 3.0 26.9 + - + +
152C LYS 4.6 4.7 - - - +
153C LEU* 3.8 14.1 - - + -
205C ILE* 3.5 31.7 - - + +
208C ILE* 3.7 34.8 - - + +
209C ARG* 4.1 32.1 - - + +
210C PRO* 4.2 16.8 - - + -
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Residues in contact with ALA 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C ALA* 3.3 20.8 + - + +
90C LEU* 1.3 78.8 - - - +
92C ALA* 1.3 57.2 + - - +
94C LYS* 3.3 13.9 + - - +
95C GLU* 3.0 28.6 + - - +
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Residues in contact with ALA 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C PHE* 3.8 26.8 - - + -
87C PHE* 4.1 22.4 - - + -
88C ALA 2.9 18.6 + - - +
89C PRO* 3.5 8.7 - - + +
91C ALA* 1.3 74.5 - - - +
93C ILE* 1.3 64.8 + - - +
95C GLU* 3.4 7.1 + - - +
96C TYR* 3.1 23.2 + - - +
147C TRP* 6.0 0.9 - - + +
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Residues in contact with ILE 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C PHE* 4.3 17.5 - - + -
89C PRO* 2.9 24.7 + - + +
90C LEU 4.0 2.7 - - - +
92C ALA* 1.3 74.3 - - - +
94C LYS* 1.3 60.9 + - - +
96C TYR* 3.3 5.9 + - + +
97C ILE* 3.0 41.2 + - + +
144C ILE* 5.8 3.8 - - + -
147C TRP* 5.3 3.4 - - + +
153C LEU* 4.5 11.0 - - + -
161C LEU* 4.4 13.9 - - + -
165C ILE* 3.7 27.1 - - + -
204C ILE* 4.4 2.9 - - + -
205C ILE* 4.0 10.1 - - + -
208C ILE* 3.4 29.8 - - + -
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Residues in contact with LYS 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C LEU* 3.0 18.1 + - + +
91C ALA* 3.3 15.7 - - - +
92C ALA 3.2 0.2 - - - -
93C ILE* 1.3 75.8 - - - +
95C GLU* 1.3 65.3 + - - +
97C ILE* 3.3 5.3 + - - +
98C ARG* 3.1 11.2 + - - +
201C GLN* 2.9 50.0 + - + +
205C ILE* 3.9 25.9 - - + +
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Residues in contact with GLU 95 (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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91C ALA 3.0 16.3 + - - +
92C ALA* 3.4 6.7 + - - +
94C LYS* 1.3 78.5 - - - +
96C TYR* 1.3 58.5 + - - +
98C ARG* 3.4 29.6 + - - +
99C LEU* 2.9 52.6 + - + +
102C GLU* 5.5 0.2 - - - +
201C GLN* 5.5 0.2 + - - -
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Residues in contact with TYR 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C TRP 3.9 17.2 + - - -
77C LEU* 5.2 0.9 - - - +
79C PRO* 3.5 26.0 - - + -
80C LEU* 3.7 36.1 - - + +
83C PHE* 4.1 20.2 - + + -
92C ALA 3.1 18.7 + - - +
93C ILE* 3.4 6.3 - - + +
95C GLU* 1.3 77.8 - - - +
97C ILE* 1.3 55.7 + - - +
99C LEU* 3.2 1.4 + - - -
100C LYS* 2.9 46.4 + - + +
162C ILE* 4.9 5.3 - - + +
165C ILE* 3.8 38.1 - - + -
166C TRP* 2.9 28.5 + - - -
212C URA 4.6 0.2 + - - -
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Residues in contact with ILE 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C ILE* 3.0 38.9 + - + +
94C LYS* 3.3 5.6 + - - +
96C TYR* 1.3 74.1 - - - +
98C ARG* 1.3 58.9 + - - +
100C LYS* 3.3 7.4 + - - +
101C LEU* 2.8 37.1 + - + +
165C ILE* 4.0 19.7 - - + -
169C THR* 3.9 4.4 - - + +
200C VAL* 3.3 28.7 - - + -
201C GLN* 4.0 26.7 - - + -
204C ILE* 3.8 30.7 - - + -
205C ILE* 4.6 3.4 - - + -
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Residues in contact with ARG 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C LYS* 3.1 17.0 + - - +
95C GLU* 3.6 26.9 + - - +
97C ILE* 1.3 79.0 - - - +
99C LEU* 1.3 58.5 + - - +
101C LEU* 3.2 7.8 + - - +
102C GLU* 2.8 47.5 + - + +
193C PHE* 4.6 7.0 - - + -
194C ASN* 4.1 19.4 - - - +
197C VAL* 3.8 32.1 - - + +
198C GLU* 5.2 4.2 + - - -
201C GLN* 3.5 31.7 + - - +
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Residues in contact with LEU 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C PRO* 3.9 32.8 - - + -
95C GLU* 2.9 43.2 + - + +
96C TYR 3.7 3.4 - - - +
98C ARG* 1.3 76.6 - - - +
100C LYS* 1.3 62.5 + - - +
102C GLU* 3.1 35.1 + - - +
103C VAL* 3.0 29.5 + - + +
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Residues in contact with LYS 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C TRP* 3.1 50.3 + - + +
79C PRO* 5.8 1.1 - - + -
96C TYR* 2.9 37.1 + - + +
97C ILE 3.6 4.7 - - - +
99C LEU* 1.3 75.6 - - + +
101C LEU* 1.3 58.7 + - - +
103C VAL* 3.2 6.9 + - + +
104C SER* 3.0 29.3 + - - -
165C ILE* 4.5 5.2 - - + -
166C TRP* 3.9 11.7 - - - +
169C THR* 3.4 27.5 + - + +
170C GLN* 2.7 31.0 + - - +
212C URA 2.9 19.4 + - - -
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Residues in contact with LEU 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C ILE* 2.8 27.1 + - + +
98C ARG 3.2 4.9 + - - +
100C LYS* 1.3 73.8 - - - +
102C GLU* 1.3 65.9 + - - +
104C SER* 3.3 3.8 + - - +
105C ARG* 3.1 16.8 + - - +
168C SER 4.8 0.2 - - - +
169C THR* 3.9 33.2 - - + +
172C TYR* 4.1 11.7 - - + -
187C LEU* 4.0 6.9 - - + +
193C PHE* 3.6 21.4 - - + -
196C THR* 4.0 20.9 - - + -
197C VAL* 3.5 41.5 - - + +
200C VAL* 4.1 10.5 - - + -
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Residues in contact with GLU 102 (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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95C GLU* 5.5 0.2 - - - +
98C ARG* 2.8 36.6 + - - +
99C LEU* 3.1 35.1 + - - +
101C LEU* 1.3 72.5 - - - +
103C VAL* 1.3 59.3 + - + +
105C ARG* 3.0 27.8 + - - +
106C ASP* 2.9 34.2 + - - +
193C PHE* 4.0 17.0 - - + -
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Residues in contact with VAL 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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72C ILE* 4.6 5.2 - - + -
75C ILE* 3.7 30.1 - - + +
76C TRP* 3.5 36.8 - - + +
99C LEU* 3.0 20.2 + - + +
100C LYS* 3.6 8.7 - - + +
102C GLU* 1.3 75.9 - - + +
104C SER* 1.3 59.5 + - - +
107C TYR* 2.8 56.2 + - + +
111C SER* 6.4 0.4 - - - -
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Residues in contact with SER 104 (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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76C TRP* 5.6 1.1 + - - +
100C LYS 3.0 13.2 + - - -
101C LEU* 3.3 9.2 + - - -
103C VAL* 1.3 76.3 - - - +
105C ARG* 1.3 61.0 + - - +
107C TYR 5.1 0.4 - - - -
108C PRO* 3.6 22.8 - - - +
111C SER* 5.1 3.3 + - - -
169C THR 2.5 33.0 + - - -
170C GLN* 3.7 10.0 - - - +
173C ALA* 3.7 20.8 - - - +
187C LEU* 3.8 17.2 - - - +
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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
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101C LEU 3.1 11.2 + - - +
102C GLU* 3.0 25.2 + - - +
104C SER* 1.3 79.1 - - - +
106C ASP* 1.3 95.1 + - - +
108C PRO* 3.6 10.6 - - - +
187C LEU* 3.4 45.5 - - + +
188C ARG* 4.3 19.2 - - + +
193C PHE* 3.7 33.8 - - + -
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Residues in contact with ASP 106 (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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102C GLU* 2.9 20.3 + - - +
105C ARG* 1.3 117.9 + - - +
107C TYR* 1.3 81.4 + - + +
108C PRO* 3.3 9.3 - - - +
109C GLN* 4.2 4.3 + - - +
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Residues in contact with TYR 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C LEU* 6.3 0.4 - - + -
72C ILE* 3.9 16.2 - - + +
75C ILE* 4.1 35.0 - - + +
103C VAL* 2.8 38.1 + - + +
106C ASP* 1.3 94.5 - - + +
108C PRO* 1.3 64.5 - - - +
109C GLN* 3.2 20.0 - - - +
110C ALA* 3.3 5.6 + - + -
111C SER* 3.2 19.1 + - - -
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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
------------------------------------------------------------
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