Contacts of the helix formed by residues 96 - 110 (chain G) 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 GLU 96 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111D ARG* 3.7 37.0 + - - +
95G ASN* 1.3 96.3 + - - +
97G LEU* 1.3 70.6 + - + +
98G GLU 2.8 6.1 + - - +
99G VAL* 3.3 6.2 + - - +
100G ARG* 3.4 21.2 + - - +
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Residues in contact with LEU 97 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D VAL* 3.5 30.1 - - + +
107D GLU* 3.3 37.0 - - + +
108D LEU* 4.3 14.8 - - + +
111D ARG* 4.0 23.5 - - - +
89F LEU* 3.7 14.8 - - + -
96G GLU* 1.3 79.7 - - + +
98G GLU* 1.3 57.4 + - - +
100G ARG* 2.9 46.2 + - - +
101G TYR* 2.5 36.0 + - - +
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Residues in contact with GLU 98 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86F GLN* 4.3 22.4 + - - +
89F LEU* 3.5 16.8 - - + +
90F GLU* 4.0 25.3 - - - +
93F ARG* 5.4 2.0 - - - +
95G ASN* 3.4 32.3 - - + +
96G GLU 2.8 1.2 - - - +
97G LEU* 1.3 76.6 - - - +
99G VAL* 1.3 66.8 + - + +
101G TYR* 3.7 4.6 - - - +
102G SER* 2.9 32.6 + - - -
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Residues in contact with VAL 99 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95G ASN* 4.2 18.4 - - + +
96G GLU 3.3 2.6 + - - +
98G GLU* 1.3 90.2 - - + +
100G ARG* 1.3 66.6 + - - +
101G TYR 3.1 0.4 - - - -
102G SER* 3.0 9.4 + - - -
103G GLU* 2.8 43.2 + - + +
106G ARG* 6.0 3.1 - - - +
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Residues in contact with ARG 100 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D ARG* 6.0 2.2 - - + -
103D GLU* 5.3 7.7 + - - -
104D VAL* 3.4 28.3 - - + +
107D GLU* 3.9 17.0 + - - +
111D ARG* 5.4 0.6 - - - +
96G GLU* 3.4 17.9 + - - +
97G LEU* 3.1 45.5 - - + +
99G VAL* 1.3 78.2 - - - +
101G TYR* 1.3 60.8 + - - +
103G GLU* 3.1 31.6 - - - +
104G VAL* 3.4 14.7 + - + +
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Residues in contact with TYR 101 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D TYR* 4.6 18.2 - + - -
104D VAL* 4.4 19.9 - - + +
105D LEU* 6.5 0.2 - - + -
83F LYS* 5.4 2.9 - - - -
85F VAL* 3.2 45.9 - - + +
86F GLN* 3.5 37.1 + - + +
89F LEU* 4.5 11.7 - - + -
97G LEU 2.5 21.3 + - - +
98G GLU 3.7 5.2 - - - +
100G ARG* 1.3 69.2 - - - +
102G SER* 1.3 59.0 + - - +
103G GLU 2.6 15.9 + - - -
104G VAL* 2.8 23.5 + - + +
105G LEU* 3.3 35.2 + - + +
85I VAL* 4.8 9.0 - - + +
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Residues in contact with SER 102 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86F GLN* 5.5 4.4 + - - -
98G GLU* 2.9 30.1 + - - -
99G VAL* 3.4 14.6 - - - -
101G TYR* 1.3 82.3 - - - +
103G GLU* 1.3 56.9 + - - +
105G LEU* 4.1 10.3 - - - +
106G ARG* 3.3 33.5 + - - +
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Residues in contact with GLU 103 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D ARG* 5.1 10.3 + - - +
99G VAL* 2.8 33.1 + - + +
100G ARG* 3.1 22.3 - - - +
101G TYR 2.6 5.5 + - - -
102G SER* 1.3 73.9 - - - +
104G VAL* 1.3 54.1 + - + +
105G LEU 2.6 16.3 + - - -
106G ARG* 3.0 20.2 + - - +
107G GLU* 2.8 29.1 + - + +
110G ARG* 5.2 0.2 + - - -
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Residues in contact with VAL 104 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D LEU* 3.7 31.9 - - + +
100D ARG* 3.6 35.0 - - + +
101D TYR* 3.8 36.3 - - + +
104D VAL* 5.2 3.4 - - + -
100G ARG* 3.4 16.8 - - + +
101G TYR* 2.8 13.5 + - + +
103G GLU* 1.3 73.2 - - + +
105G LEU* 1.3 57.2 + - - +
107G GLU 4.4 1.1 - - - -
108G LEU* 3.3 25.4 - - + +
89I LEU* 5.7 0.2 - - + -
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Residues in contact with LEU 105 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86F GLN* 6.4 0.2 - - - +
101G TYR* 3.3 41.4 + - + +
102G SER* 4.1 9.2 - - - +
103G GLU 2.6 7.5 + - - -
104G VAL* 1.3 75.2 - - - +
106G ARG* 1.3 61.0 + - + +
107G GLU 3.1 1.1 - - - -
108G LEU* 3.0 6.8 + - + +
109G GLU* 2.8 41.5 + - + +
163H ALA 6.1 2.9 - - - +
166H GLU* 5.5 4.7 - - - +
167H ILE* 5.4 11.7 - - + -
85I VAL* 6.2 4.0 - - + -
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Residues in contact with ARG 106 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99G VAL* 6.0 2.7 - - - +
102G SER* 3.3 24.2 + - - +
103G GLU* 3.0 19.8 + - - +
105G LEU* 1.3 73.5 - - + +
107G GLU* 1.3 56.5 + - - +
108G LEU 3.0 7.8 + - - -
109G GLU* 3.4 18.9 + - - +
110G ARG* 3.0 49.7 + - - +
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Residues in contact with GLU 107 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D LEU* 2.8 41.2 - - + +
100D ARG* 3.5 27.0 + - - +
103G GLU* 2.8 20.1 + - + +
104G VAL 4.5 0.4 - - - -
105G LEU 4.2 0.2 - - - -
106G ARG* 1.3 75.1 - - - +
108G LEU* 1.3 52.0 + - - +
110G ARG* 3.3 30.8 + - - +
111G ARG* 3.5 31.1 + - - +
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Residues in contact with LEU 108 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D LEU* 3.5 17.9 - - + -
104G VAL* 3.3 24.9 - - + +
105G LEU* 3.3 8.5 - - + +
106G ARG 3.1 0.2 + - - -
107G GLU* 1.3 79.0 - - - +
109G GLU* 1.3 63.3 + - - +
110G ARG 3.2 2.8 - - - +
111G ARG* 4.0 17.3 - - + -
112G ILE* 3.2 20.3 - - + +
167H ILE* 4.9 11.5 - - + +
85I VAL* 5.3 8.1 - - + -
88I ILE* 4.0 22.0 - - + +
89I LEU* 4.0 18.4 - - + -
92I VAL* 3.9 26.7 - - + -
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Residues in contact with GLU 109 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105G LEU* 2.8 27.9 + - + +
106G ARG* 3.4 15.3 + - - +
108G LEU* 1.3 78.9 - - - +
110G ARG* 1.3 60.6 + - + +
112G ILE* 4.2 6.0 - - - +
113G ILE* 3.2 25.0 + - + +
166H GLU* 4.7 22.3 - - - +
167H ILE* 5.8 1.3 - - - -
170H ARG* 5.5 4.0 + - - +
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Residues in contact with ARG 110 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103G GLU* 5.2 0.4 + - - +
106G ARG* 3.0 53.4 + - - +
107G GLU* 3.3 39.1 + - - +
108G LEU 4.9 0.7 - - - +
109G GLU* 1.3 81.0 - - + +
111G ARG* 1.3 50.8 + - - +
112G ILE 2.7 4.9 + - - -
113G ILE* 2.6 11.9 + - - +
114G HIS* 2.6 37.1 + - + +
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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
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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