Contacts of the helix formed by residues 88 - 107 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A ASP 3.8 1.4 + - - -
87A PHE* 1.3 69.4 - - - +
89A PRO* 1.3 64.3 - - + +
90A LEU* 3.4 2.5 - - + +
91A ALA* 3.3 20.6 + - + +
92A ALA* 2.9 28.2 + - - +
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Residues in contact with PRO 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A PHE* 5.7 0.2 - - - -
87A PHE 3.1 8.5 - - - +
88A ALA* 1.3 81.8 - - + +
90A LEU* 1.3 58.5 + - + +
92A ALA* 3.3 5.1 + - + +
93A ILE* 2.9 38.1 + - - +
147A TRP* 3.3 60.3 - - + +
152A LYS* 4.1 26.0 - - + +
153A LEU* 4.3 11.7 - - + -
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Residues in contact with LEU 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ALA 3.4 0.4 - - - -
89A PRO* 1.3 73.2 - - + +
91A ALA* 1.3 68.9 + - - +
92A ALA 3.1 0.2 + - - -
93A ILE* 3.2 2.4 + - - -
94A LYS* 2.8 26.7 + - - +
152A LYS 5.0 4.9 - - - +
153A LEU* 3.5 29.6 - - + -
205A ILE* 3.8 23.3 - - + +
208A ILE* 4.1 15.9 - - + -
209A ARG* 3.5 47.1 - - + +
210A PRO* 4.9 4.9 - - + -
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Residues in contact with ALA 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ALA* 3.3 26.8 - - + +
90A LEU* 1.3 80.1 - - - +
92A ALA* 1.3 56.5 + - - +
94A LYS* 3.4 10.8 - - - +
95A GLU* 3.2 26.5 + - - +
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Residues in contact with ALA 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A PHE* 4.0 24.7 - - + -
87A PHE* 4.3 23.3 - - + -
88A ALA 2.9 16.4 + - - +
89A PRO* 3.6 7.2 - - + +
91A ALA* 1.3 73.2 - - - +
93A ILE* 1.3 62.6 + - - +
95A GLU* 3.5 6.5 + - - +
96A TYR* 3.0 28.8 + - - +
147A TRP* 6.1 0.7 - - + +
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Residues in contact with ILE 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A PHE* 4.3 17.5 - - + -
89A PRO* 2.9 24.6 + - + +
90A LEU* 3.8 3.4 - - - +
92A ALA* 1.3 73.2 - - - +
94A LYS* 1.3 66.8 + - - +
96A TYR* 3.2 6.8 + - - +
97A ILE* 3.0 25.6 + - + +
144A ILE* 5.5 2.5 - - + -
147A TRP* 5.0 4.3 - - + -
153A LEU* 4.0 17.5 - - + -
161A LEU* 3.9 14.4 - - + -
165A ILE* 4.1 22.7 - - + -
204A ILE* 4.5 7.2 - - + -
205A ILE* 3.8 16.6 - - + -
208A ILE* 3.7 28.5 - - + -
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Residues in contact with LYS 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A LEU 2.8 18.0 + - - +
91A ALA* 3.4 15.7 - - - +
93A ILE* 1.3 74.1 - - - +
95A GLU* 1.3 61.7 + - - +
97A ILE* 3.2 8.7 + - - +
98A ARG 3.2 1.6 + - - -
201A GLN* 2.8 50.5 + - + +
205A ILE* 3.8 22.1 - - + +
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Residues in contact with GLU 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A ALA 3.2 12.6 + - - +
92A ALA* 4.0 6.9 - - - +
93A ILE 3.3 0.2 - - - -
94A LYS* 1.3 77.3 - - - +
96A TYR* 1.3 66.4 + - - +
98A ARG* 3.2 35.6 + - - +
99A LEU* 2.9 42.8 + - + +
201A GLN* 4.9 0.2 - - - +
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Residues in contact with TYR 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A TRP 4.2 11.3 + - - -
77A LEU* 5.4 0.3 - - - +
79A PRO* 3.7 26.2 - - + -
80A LEU* 3.5 35.6 - - + +
83A PHE* 4.0 21.8 - + + -
92A ALA 3.0 19.0 + - - +
93A ILE* 3.5 6.3 - - - +
95A GLU* 1.3 76.3 - - - +
97A ILE* 1.3 62.7 + - - +
99A LEU* 3.4 1.1 + - - -
100A LYS* 2.9 42.9 + - + +
162A ILE* 4.5 5.8 - - + +
165A ILE* 3.9 36.1 - - + -
166A TRP* 2.9 28.8 + - - -
212A URA 4.7 1.6 + - - -
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Residues in contact with ILE 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A ILE* 3.0 22.1 + - + +
94A LYS 3.4 7.2 - - - +
95A GLU 3.2 0.2 - - - -
96A TYR* 1.3 77.7 - - - +
98A ARG* 1.3 63.3 + - - +
100A LYS* 3.7 2.2 - - - +
101A LEU* 3.1 35.4 + - + +
165A ILE* 4.3 20.4 - - + -
169A THR* 4.0 7.8 - - + +
200A VAL* 3.5 23.6 - - + -
201A GLN* 3.8 30.3 - - + -
204A ILE* 3.9 40.4 - - + -
205A ILE* 4.7 3.8 - - + -
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Residues in contact with ARG 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A LYS 3.2 3.1 + - - +
95A GLU* 3.2 46.8 + - - +
97A ILE* 1.3 80.4 - - - +
99A LEU* 1.3 82.7 + - - +
101A LEU* 3.3 3.1 + - - +
102A GLU* 2.9 52.3 + - + +
193A PHE* 4.7 4.4 - - + -
197A VAL* 4.3 25.8 - - + -
201A GLN* 3.9 15.2 - - - +
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Residues in contact with LEU 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A PRO* 3.9 33.2 - - + -
95A GLU* 2.9 38.0 + - + +
96A TYR* 4.0 2.7 - - - +
98A ARG* 1.3 98.5 - - - +
100A LYS* 1.3 64.4 + - - +
102A GLU* 3.0 33.0 + - + +
103A VAL* 3.0 22.8 + - + +
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Residues in contact with LYS 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A TRP* 3.2 44.0 - - + +
79A PRO* 5.8 1.1 - - + -
96A TYR* 2.9 40.2 + - + +
97A ILE* 3.7 2.5 - - - +
99A LEU* 1.3 75.9 - - + +
101A LEU* 1.3 58.3 + - - +
103A VAL* 3.2 11.3 + - + +
104A SER* 3.0 26.9 + - - -
165A ILE* 4.5 4.0 - - + -
166A TRP* 3.9 9.9 - - - +
169A THR* 3.4 29.7 - - + +
170A GLN* 2.7 25.7 + - - +
212A URA 2.5 31.9 + - - +
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Residues in contact with LEU 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A ILE* 3.1 30.9 + - + +
98A ARG 3.7 3.4 - - - +
100A LYS* 1.3 73.1 - - - +
102A GLU* 1.3 60.6 + - - +
104A SER* 3.2 5.7 + - - -
105A ARG* 2.9 28.1 + - - +
168A SER 5.0 0.2 - - - -
169A THR* 3.6 34.5 - - + +
172A TYR* 3.8 24.2 - - + -
187A LEU* 3.9 6.6 - - + +
193A PHE* 3.7 10.0 - - + -
196A THR* 4.0 13.5 - - + +
197A VAL* 3.7 43.7 - - + +
200A VAL* 4.3 5.6 - - + -
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Residues in contact with GLU 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A ARG* 2.9 51.7 + - + +
99A LEU* 3.2 32.0 - - - +
101A LEU* 1.3 76.5 - - - +
103A VAL* 1.3 56.5 + - + +
105A ARG* 3.1 26.2 + - - +
106A ASP* 2.9 34.8 + - - +
193A PHE* 3.9 19.6 - - + -
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Residues in contact with VAL 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A ILE* 4.7 7.2 - - + -
75A ILE* 4.2 22.0 - - + +
76A TRP* 3.4 40.4 - - + +
79A PRO* 6.5 0.7 - - + -
99A LEU* 3.0 21.5 + - + +
100A LYS* 3.2 10.0 + - + +
102A GLU* 1.3 74.4 - - + +
104A SER* 1.3 62.1 + - - +
106A ASP* 4.6 0.7 - - - -
107A TYR* 2.7 53.1 + - + +
111A SER* 5.7 0.6 - - - -
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Residues in contact with SER 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A TRP* 5.8 0.5 + - - -
100A LYS 3.0 12.0 + - - -
101A LEU 3.4 10.5 - - - -
103A VAL* 1.3 76.4 - - - +
105A ARG* 1.3 65.7 + - - +
107A TYR 5.1 0.2 - - - -
108A PRO* 3.5 22.4 - - - +
111A SER* 4.9 4.1 + - - -
169A THR 2.8 28.5 + - - -
170A GLN* 3.5 14.0 - - - +
173A ALA* 3.7 18.9 - - - +
187A LEU* 3.8 16.0 - - - +
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Residues in contact with ARG 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A LEU 2.9 13.4 + - - +
102A GLU* 3.1 26.0 + - - +
104A SER* 1.3 78.9 - - - +
106A ASP* 1.3 89.2 + - - +
108A PRO* 3.6 9.4 - - - +
187A LEU* 3.6 40.8 - - + +
188A ARG* 4.5 21.5 + - + +
193A PHE* 3.6 38.3 - - + -
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Residues in contact with ASP 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A GLU* 2.9 19.2 + - - +
104A SER 3.3 0.2 - - - -
105A ARG* 1.3 115.3 + - - +
107A TYR* 1.3 83.0 + - + +
108A PRO* 3.3 9.7 - - - +
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Residues in contact with TYR 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ILE* 3.9 18.6 - - + +
75A ILE* 4.3 33.4 - - + +
103A VAL* 2.7 34.1 + - + +
106A ASP* 1.3 96.6 - - + +
108A PRO* 1.3 64.0 - - - +
109A GLN* 3.3 3.1 - - - -
110A ALA* 3.3 10.3 + - + +
111A SER* 3.0 20.6 + - - -
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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