Contacts of the helix formed by residues 86 - 102 (chain I) in PDB entry 1LWU
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 GLN 86 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D TYR* 3.7 27.5 + - - +
102D SER* 4.4 7.3 + - - -
105D LEU* 5.3 3.3 - - - +
163E ALA* 5.5 9.0 - - + +
164E GLN 6.0 0.2 - - - +
83I LYS* 3.4 29.6 - - - +
84I THR 3.0 1.2 - - - +
85I VAL* 1.3 82.0 - - - +
87I LYS* 1.3 72.0 + - + +
89I LEU* 3.8 7.0 + - - +
90I GLU* 3.7 23.4 + - - +
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Residues in contact with LYS 87 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83I LYS* 4.6 11.4 - - - +
84I THR 3.7 6.7 + - - +
86I GLN* 1.3 84.1 - - + +
88I ILE* 1.3 55.5 + - + +
89I LEU 2.6 16.8 + - - -
90I GLU* 2.6 34.2 + - + +
91I GLU* 2.7 48.1 + - + +
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Residues in contact with ILE 88 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108G LEU* 4.0 10.2 - - + +
163H ALA 3.0 36.6 - - - +
164H GLN* 3.9 10.3 - - - +
167H ILE* 3.2 49.6 - - + +
168H GLU* 5.7 3.1 - - - +
84I THR 3.0 23.6 - - - +
85I VAL* 3.4 31.2 - - + +
86I GLN 3.4 0.2 - - - -
87I LYS* 1.3 76.0 - - + +
89I LEU* 1.3 56.7 + - - +
91I GLU* 4.6 10.8 - - - +
92I VAL* 3.7 17.6 - - - +
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Residues in contact with LEU 89 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D LEU* 3.1 35.7 - - + +
98D GLU* 3.3 31.2 - - + -
101D TYR* 5.1 13.5 - - + -
104G VAL* 5.7 0.4 - - + -
108G LEU* 4.0 25.6 - - + -
111G ARG* 5.6 1.8 - - - +
85I VAL* 3.8 13.2 + - + +
86I GLN* 3.8 8.9 + - - +
87I LYS 2.6 5.7 + - - -
88I ILE* 1.3 76.9 - - - +
90I GLU* 1.3 66.5 + - + +
91I GLU 3.5 0.4 - - - -
92I VAL* 3.5 17.2 - - + +
93I ARG* 3.6 11.4 + - + +
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Residues in contact with GLU 90 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86I GLN* 3.7 18.8 + - - +
87I LYS* 2.6 44.3 + - - +
89I LEU* 1.3 82.2 - - + +
91I GLU* 1.3 60.5 + - + +
92I VAL 3.0 2.2 - - - -
93I ARG* 2.8 37.9 + - + +
94I ILE* 3.1 14.3 + - + +
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Residues in contact with GLU 91 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167H ILE* 4.2 8.7 - - + +
168H GLU* 4.9 7.8 - - - +
171H TYR* 2.9 62.1 + - + +
87I LYS* 2.7 44.2 + - + +
88I ILE* 4.6 8.2 - - - +
90I GLU* 1.3 72.9 - - + +
92I VAL* 1.3 62.6 - - + +
94I ILE* 2.9 21.3 + - - +
95I LEU* 3.0 19.3 + - - +
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Residues in contact with VAL 92 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108G LEU* 3.9 12.6 - - + -
111G ARG* 3.7 23.8 - - + +
112G ILE* 3.3 31.6 - - + -
115G LEU* 4.9 7.2 - - + -
167H ILE* 5.7 1.1 - - + -
88I ILE 3.7 20.0 - - - +
89I LEU* 3.5 11.2 + - + +
90I GLU 3.0 0.4 - - - -
91I GLU* 1.3 77.9 - - + +
93I ARG* 1.3 51.2 + - - +
95I LEU* 4.6 1.3 - - - +
96I GLU* 2.7 65.8 + - + +
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Residues in contact with ARG 93 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D ASN* 3.2 48.4 - - - +
98D GLU* 4.4 9.3 - - - +
89I LEU* 3.6 9.2 + - + +
90I GLU* 2.8 27.6 + - + +
92I VAL* 1.3 79.8 - - - +
94I ILE* 1.3 52.4 + - + +
96I GLU* 4.0 9.7 - - - +
97I GLN* 2.8 36.9 + - - +
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Residues in contact with ILE 94 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171H TYR* 5.4 1.3 - - - +
175H LYS* 3.8 17.5 - - - +
90I GLU* 3.1 18.6 + - + +
91I GLU* 3.1 13.2 - - - +
92I VAL 2.9 2.0 + - - -
93I ARG* 1.3 77.6 - - + +
95I LEU* 1.3 70.8 + - + +
96I GLU 3.1 1.1 - - - -
97I GLN* 2.8 20.7 + - - +
98I ILE* 2.5 48.4 + - + +
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Residues in contact with LEU 95 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112G ILE* 6.5 0.4 - - + -
115G LEU* 3.3 25.0 - - + +
119G ILE* 4.4 1.0 - - + +
171H TYR* 3.6 18.8 - - + -
174H VAL* 3.2 42.6 - - + -
175H LYS* 3.9 22.9 - - + +
178H ILE* 3.6 29.6 - - + +
91I GLU 3.0 14.5 + - - +
92I VAL* 5.1 0.7 - - - -
94I ILE* 1.3 84.9 - - + +
96I GLU* 1.3 56.3 + - - +
97I GLN 3.0 5.6 - - - -
98I ILE* 3.9 1.6 - - + +
99I GLY* 3.0 25.5 + - - -
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Residues in contact with GLU 96 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111G ARG* 3.1 48.2 + - - +
114G HIS* 4.9 3.8 - - - -
115G LEU* 3.1 19.2 - - + +
118G ARG* 3.2 36.3 + - - +
92I VAL* 2.7 39.3 + - + +
93I ARG* 4.0 9.3 - - - +
95I LEU* 1.3 71.6 - - - +
97I GLN* 1.3 57.8 + - - +
99I GLY 4.4 0.9 - - - -
100I VAL* 3.5 9.0 - - - +
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Residues in contact with GLN 97 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93I ARG 2.8 19.9 + - - +
94I ILE* 2.8 27.7 + - - +
96I GLU* 1.3 80.4 - - - +
98I ILE* 1.3 58.1 + - + +
99I GLY 3.1 1.3 - - - -
100I VAL* 2.8 27.9 + - - +
101I SER* 3.2 10.7 + - - -
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Residues in contact with ILE 98 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175H LYS* 4.7 10.1 - - - +
178H ILE* 3.1 50.0 - - + -
179H GLU* 6.3 0.2 - - + -
94I ILE* 2.5 40.0 + - + +
95I LEU* 4.3 0.7 - - + -
97I GLN* 1.3 77.3 - - - +
99I GLY* 1.3 54.3 + - - +
101I SER* 2.9 10.5 + - - -
102I HIS* 2.5 48.1 + - + +
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Residues in contact with GLY 99 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115G LEU* 5.4 3.1 - - - -
118G ARG* 5.0 9.6 - - - -
119G ILE* 5.2 6.5 - - - -
122G GLN* 2.8 30.8 + - - -
178H ILE* 5.1 3.6 - - - -
95I LEU 3.0 20.2 + - - -
96I GLU* 5.0 0.7 - - - -
97I GLN 3.1 0.2 - - - -
98I ILE* 1.3 78.4 - - - +
100I VAL* 1.3 61.0 + - - +
102I HIS* 3.8 8.3 - - - -
103I ASP* 2.9 7.0 - - - +
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Residues in contact with VAL 100 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118G ARG* 4.0 12.6 - - - +
96I GLU 3.5 22.7 - - - +
97I GLN* 2.8 11.0 + - - +
99I GLY* 1.3 78.9 - - - +
101I SER* 1.3 60.4 + - - +
102I HIS 3.3 0.7 - - - -
103I ASP* 3.5 8.9 - - + -
104I ALA* 3.0 24.6 + - - +
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Residues in contact with SER 101 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97I GLN* 3.2 10.0 + - - -
98I ILE* 2.9 13.6 + - - -
100I VAL* 1.3 74.3 - - - +
102I HIS* 1.3 63.7 + - - +
103I ASP 3.1 1.1 - - - -
104I ALA* 3.3 15.0 + - - +
105I GLN* 3.3 24.5 + - - +
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Residues in contact with HIS 102 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119G ILE* 6.0 1.1 - - + -
122G GLN* 3.2 25.6 - - + +
126G LEU* 5.5 1.1 - - + -
178H ILE* 3.0 32.8 + - + -
182H VAL* 2.8 55.9 - - + +
183H ALA* 3.7 7.4 - - + -
186H LEU* 4.1 17.1 - - + +
98I ILE* 2.5 33.1 + - + +
99I GLY* 3.8 2.5 - - - -
101I SER* 1.3 74.1 - - - +
103I ASP* 1.3 54.2 + - - +
104I ALA 3.3 1.2 + - - -
105I GLN* 4.3 3.4 + - - -
106I ILE* 3.2 28.2 + - - +
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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