Contacts of the helix formed by residues 101 - 115 (chain G) in PDB entry 1RZR
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 ASN 101 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98G SER 3.1 20.1 + - - +
99G ASP* 2.4 31.1 + - - +
100G GLN* 1.3 65.1 - - - +
102G GLN* 1.3 74.1 + - - +
103G ASP* 2.1 51.8 + - - +
104G LYS* 3.0 18.5 + - - +
105G GLU* 2.9 10.5 + - - +
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Residues in contact with GLN 102 (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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100G GLN 3.4 5.1 + - - +
101G ASN* 1.3 101.6 - - - +
103G ASP* 1.3 59.2 + - + +
104G LYS 3.6 0.2 - - - -
105G GLU* 2.8 12.8 + - - +
106G LEU* 2.7 35.9 + - - +
128G THR* 4.7 11.2 - - + -
130G GLU* 5.2 2.8 - - - +
131G HIS* 4.3 12.1 - - + -
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Residues in contact with ASP 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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101G ASN* 2.1 41.2 + - - +
102G GLN* 1.3 79.4 - - + +
104G LYS* 1.3 84.8 + - - +
106G LEU* 3.1 14.8 + - - +
107G HIS* 3.1 13.0 + - - +
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Residues in contact with LYS 104 (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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80C ARG* 5.2 2.4 - - - +
83C GLU* 5.2 3.4 + - - -
84C ASP* 5.4 2.8 + - - -
87C THR* 4.9 17.7 + - - +
96G SER* 5.2 2.6 + - - -
97G ASN* 3.2 23.1 + - - +
98G SER* 3.4 29.8 - - - +
99G ASP* 3.6 13.0 + - + +
101G ASN* 3.0 9.5 + - - +
103G ASP* 1.3 87.5 + - - +
105G GLU* 1.3 69.4 + - - +
106G LEU 2.9 1.6 - - - -
107G HIS* 2.6 22.0 + - + +
108G LEU* 2.8 24.2 + - + +
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Residues in contact with GLU 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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66G ILE* 4.1 13.9 - - + -
98G SER* 3.7 24.6 + - - +
100G GLN* 3.7 10.3 - - - +
101G ASN 2.9 6.1 + - - -
102G GLN* 2.8 35.0 + - - -
103G ASP 3.4 0.2 - - - -
104G LYS* 1.3 80.0 - - - +
106G LEU* 1.3 70.9 + - + +
108G LEU* 3.7 2.1 + - - +
109G LEU* 3.3 28.9 + - - +
122G PHE* 3.5 25.2 - - + -
123G MSE 5.7 0.2 - - - +
124G SER* 3.0 32.4 + - - -
126G ASN 5.1 0.3 - - - +
131G HIS* 3.8 11.7 + - - +
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Residues in contact with LEU 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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102G GLN 2.7 26.2 - - - +
103G ASP* 3.1 9.6 + - - +
104G LYS 2.7 1.8 + - - -
105G GLU* 1.3 82.0 - - + +
107G HIS* 1.3 59.4 + - - +
109G LEU* 3.9 8.8 + - + +
110G ASN* 2.7 27.6 + - - +
122G PHE* 5.7 0.9 - - + -
130G GLU* 2.7 42.8 - - + +
131G HIS* 3.6 27.4 - - + +
134G GLU* 4.7 15.9 - - + +
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Residues in contact with HIS 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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90C LYS* 3.3 29.5 + - - -
846C SO4 3.4 15.4 + - - -
103G ASP 3.1 10.1 + - - +
104G LYS* 2.6 19.9 + - + +
106G LEU* 1.3 71.9 - - - +
108G LEU* 1.3 71.3 + - + +
109G LEU 3.2 0.2 - - - -
110G ASN* 3.3 7.2 + - - +
111G ASN* 3.1 28.3 + - + +
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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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846C SO4 3.7 21.1 - - - +
66G ILE* 3.6 35.0 - - + -
96G SER* 3.6 46.9 - - - +
97G ASN 3.9 14.1 - - - +
98G SER* 4.2 6.5 - - - -
104G LYS* 2.8 23.0 + - + +
105G GLU 4.0 0.9 - - - +
107G HIS* 1.3 83.9 - - + +
109G LEU* 1.3 54.3 + - - +
111G ASN* 3.1 5.0 + - - +
112G MSE 2.7 43.4 + - + +
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Residues in contact with LEU 109 (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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66G ILE* 3.8 9.4 - - + -
105G GLU 3.3 14.8 + - - +
106G LEU* 4.0 8.7 - - + +
107G HIS 3.2 0.6 - - - -
108G LEU* 1.3 79.3 - - - +
110G ASN* 1.3 60.9 + - - +
112G MSE 3.5 4.0 - - - +
113G LEU* 2.8 58.6 + - + +
120G ILE* 4.2 16.8 - - + -
122G PHE* 3.3 41.1 - - + -
134G GLU* 4.5 13.9 - - + +
135G LEU* 3.9 23.6 - - + -
138G SER* 4.9 3.8 - - - -
142G VAL* 6.1 0.7 - - + -
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Residues in contact with ASN 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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47C ARG* 3.8 27.3 + - + +
106G LEU* 2.7 27.9 + - - +
107G HIS* 3.3 6.5 + - - +
108G LEU 3.3 0.2 - - - -
109G LEU* 1.3 78.5 - - - +
111G ASN* 1.3 58.6 + - - +
113G LEU* 4.1 5.9 - - - +
114G GLY* 2.7 29.1 + - - -
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Residues in contact with ASN 111 (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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90C LYS* 5.1 4.8 - - - +
92C ASN* 2.7 33.2 + - - -
846C SO4 2.7 34.7 + - - +
107G HIS* 3.1 28.0 + - + +
108G LEU* 3.1 3.8 + - - +
110G ASN* 1.3 76.1 - - - +
112G MSE 1.3 78.8 + - - +
114G GLY* 3.8 0.6 - - - -
115G LYS* 2.9 34.0 + - - +
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Residues in contact with MSE 112 (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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92C ASN* 3.9 13.0 - - - +
64G GLY* 3.3 35.9 - - - -
65G VAL 3.7 11.7 - - - +
66G ILE* 3.7 22.4 - - + -
94G ILE* 4.1 12.1 - - + +
96G SER* 4.8 9.0 - - - +
108G LEU* 2.7 28.2 + - + +
109G LEU* 3.5 6.3 - - - +
111G ASN* 1.3 104.6 + - - +
113G LEU* 1.3 54.7 + - - +
115G LYS* 2.6 34.5 + - - +
116G GLN 3.0 4.3 + - - -
117G VAL* 3.6 18.3 + - + +
120G ILE* 4.7 5.8 - - + -
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Residues in contact with LEU 113 (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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1C MSE 5.4 0.4 - - + -
47C ARG* 2.9 34.8 - - - +
109G LEU* 2.8 49.1 + - + +
110G ASN* 4.0 2.7 - - - +
112G MSE 1.3 70.9 - - - +
114G GLY* 1.3 49.5 + - - +
116G GLN* 2.4 38.3 + - - -
117G VAL* 4.1 5.8 - - + +
120G ILE* 4.1 8.1 - - + -
134G GLU 5.7 0.7 - - - +
138G SER* 3.9 7.0 - - - +
139G PRO* 3.2 34.5 - - + -
140G VAL* 3.6 26.0 - - + -
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Residues in contact with GLY 114 (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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47C ARG* 3.6 11.5 - - - +
48C PRO* 3.7 16.3 - - - +
49C ASN* 3.6 0.3 + - - -
50C ALA* 2.9 27.0 + - - -
110G ASN 2.7 21.9 + - - -
111G ASN 3.8 0.7 - - - -
113G LEU* 1.3 69.0 - - - +
115G LYS* 1.3 56.6 + - - +
116G GLN* 2.8 23.7 + - - +
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Residues in contact with LYS 115 (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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50C ALA* 3.5 24.5 - - + +
51C VAL* 3.6 11.9 - - + +
60C THR* 4.5 15.0 - - - +
61C THR* 4.5 5.5 + - - -
62C THR* 4.4 12.1 - - + +
92C ASN* 2.5 48.8 + - - +
115C LYS* 5.9 3.7 + - - +
60G THR* 4.3 3.5 - - - +
94G ILE* 3.5 25.8 - - + +
111G ASN* 2.9 15.4 + - - +
112G MSE 2.6 21.0 + - - +
114G GLY* 1.3 71.5 - - - +
116G GLN* 1.3 69.1 - - - +
117G VAL 4.9 1.3 - - - +
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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