Contacts of the helix formed by residues 129 - 144 (chain B) in PDB entry 1RLI
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 GLY 129 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78B ILE* 4.9 11.7 - - - -
81B PHE 5.3 2.0 - - - -
125B PRO* 2.8 23.5 + - - +
128B LYS* 1.3 76.1 - - - +
130B LEU* 1.3 64.4 + - - +
131B PRO* 3.3 2.5 - - - -
132B LEU* 3.2 21.5 + - - +
133B ILE* 3.2 14.9 + - - +
152B LEU* 4.3 12.7 - - - +
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Residues in contact with LEU 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B LYS 3.7 8.7 - - - +
127B ILE* 3.3 18.2 - - + +
128B LYS 3.3 0.4 - - - -
129B GLY* 1.3 75.6 - - - +
131B PRO* 1.3 74.8 - - + +
133B ILE* 3.0 7.8 + - + +
134B GLN* 2.9 26.4 + - - +
150B TYR* 5.0 2.7 - - + -
152B LEU* 3.8 12.8 - - + -
130D LEU* 3.9 29.3 - - + +
133D ILE* 3.6 36.6 - - + -
134D GLN* 4.1 21.5 - - + +
150D TYR* 3.4 22.9 - - - +
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Residues in contact with PRO 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B PHE 5.2 1.3 - - - +
127B ILE 4.5 0.7 - - - +
128B LYS 3.6 11.2 - - - +
129B GLY 3.6 3.4 - - - -
130B LEU* 1.3 93.0 - - + +
132B LEU* 1.3 57.0 + - - +
134B GLN* 3.0 14.7 + - - +
135B GLN* 2.9 28.3 + - - +
131C PRO* 3.6 27.0 - - + +
134C GLN* 3.8 15.9 - - + -
135C GLN* 4.1 12.3 - - + +
138C HIS* 4.0 19.1 - - + +
134D GLN* 3.4 19.1 - - - +
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Residues in contact with LEU 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B THR* 4.9 1.3 - - + -
78B ILE* 4.3 21.5 - - + -
81B PHE 3.8 15.7 + - - +
82B GLY* 3.7 23.8 - - - +
83B MET* 3.5 39.7 - - + +
119B ALA* 4.5 11.2 - - + -
129B GLY* 3.2 12.4 + - - +
130B LEU 3.2 0.4 - - - -
131B PRO* 1.3 80.6 - - - +
133B ILE* 1.3 63.7 + - + +
135B GLN* 3.2 17.8 + - - +
136B PHE* 2.9 40.0 + - + -
152B LEU* 5.4 2.0 - - + -
135C GLN* 4.7 3.3 - - - +
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Residues in contact with ILE 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B VAL* 4.0 20.6 - - + -
129B GLY 3.2 12.7 + - - +
130B LEU* 3.0 10.2 + - + +
132B LEU* 1.3 80.5 - - + +
134B GLN* 1.3 57.1 + - - +
136B PHE* 3.3 6.7 + - + +
137B GLU* 2.9 25.8 + - - +
147B PHE* 3.6 9.9 - - + -
150B TYR* 3.8 51.4 - - + -
151B VAL 5.7 0.2 - - - +
152B LEU* 3.8 28.3 - - + -
127D ILE* 4.2 2.0 - - + -
130D LEU* 3.8 22.4 - - + -
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Residues in contact with GLN 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A GLN* 3.4 19.8 + - - +
130B LEU 2.9 11.9 + - - +
131B PRO* 3.0 18.7 + - - +
133B ILE* 1.3 74.3 - - - +
135B GLN* 1.3 65.1 + - - +
137B GLU* 3.2 10.2 + - - +
138B HIS* 3.0 31.0 + - + +
131C PRO* 3.6 13.8 - - + +
134C GLN* 3.3 24.9 + - - -
127D ILE* 5.3 4.0 - - + +
130D LEU* 4.0 26.2 - - + +
131D PRO* 4.0 7.3 - - - +
134D GLN* 3.3 22.0 + - - +
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Residues in contact with GLN 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B MET* 4.5 10.1 - - - -
88B LYS* 5.4 1.8 - - - +
131B PRO 2.9 12.9 + - - +
132B LEU* 3.2 14.6 + - + +
134B GLN* 1.3 77.2 - - - +
136B PHE* 1.3 63.4 + - + +
138B HIS* 3.2 9.6 + - - +
139B ILE* 3.0 32.1 + - + +
603B PT 2.7 29.7 - - - -
80C TRP 4.0 9.3 + - - +
81C PHE* 3.2 31.7 - - + +
82C GLY* 3.6 15.2 - - - -
131C PRO* 4.2 8.7 - - + +
132C LEU* 5.0 5.2 + - - +
135C GLN* 3.8 22.1 + - - +
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Residues in contact with PHE 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B PHE* 4.3 13.7 - + + -
76B THR* 4.4 4.9 - - + -
83B MET* 3.1 44.0 - - + -
87B LEU* 3.8 9.6 - - + -
91B ILE* 4.1 12.8 - - + -
117B VAL* 3.5 38.6 - - + -
132B LEU* 2.9 35.7 + - + -
133B ILE* 3.6 9.4 - - - +
135B GLN* 1.3 74.1 - - - +
137B GLU* 1.3 59.3 + - - +
139B ILE* 3.2 12.4 + - + +
140B PHE* 2.8 65.2 + + + -
147B PHE* 4.1 3.6 - - + -
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Residues in contact with GLU 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B ILE 2.9 13.4 + - - +
134B GLN* 3.2 13.2 + - - +
136B PHE* 1.3 78.0 - - - +
138B HIS* 1.3 77.4 + - - +
140B PHE* 4.0 2.1 - - - +
141B HIS* 3.0 41.2 + - - +
147B PHE* 3.7 26.8 - - + +
127D ILE* 3.5 33.2 - - + +
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Residues in contact with HIS 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A GLN* 5.8 0.8 + - - -
134B GLN* 3.0 22.7 + - + +
135B GLN* 3.2 5.4 + - - +
137B GLU* 1.3 88.8 + - - +
139B ILE* 1.3 59.7 + - - +
141B HIS* 3.4 6.9 + - - +
142B PHE* 2.9 24.3 + - - +
81C PHE* 3.3 40.5 - + + -
127C ILE* 4.7 5.6 + - + -
128C LYS* 3.7 49.7 - - + +
131C PRO* 4.0 19.3 - - + +
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Residues in contact with ILE 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B MET* 5.0 1.6 - - + -
91B ILE* 4.2 23.3 - - + -
94B TRP* 4.0 21.8 - - + -
135B GLN* 3.0 35.6 + - + +
136B PHE* 3.6 20.4 - - + +
138B HIS* 1.3 74.3 - - - +
140B PHE* 1.3 74.5 + - + +
142B PHE* 3.3 5.5 + - - +
143B MET* 3.1 21.8 + - - +
80C TRP* 3.5 45.7 - - + +
81C PHE* 3.9 9.9 - - + -
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Residues in contact with PHE 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B PHE* 3.7 42.0 - + - -
91B ILE* 6.2 0.4 - - + -
94B TRP* 5.2 1.6 - + - -
115B ALA* 3.8 15.9 - - + -
117B VAL* 3.8 15.7 - - + -
136B PHE* 2.8 47.2 + + + +
137B GLU 4.0 2.5 - - - +
139B ILE* 1.3 83.3 - - + +
141B HIS* 1.3 56.9 + - - +
143B MET* 3.1 2.4 + - - -
144B GLY 2.8 8.7 + - - -
145B MET* 2.8 60.6 + - + +
147B PHE* 3.6 42.6 - + + -
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Residues in contact with HIS 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B GLU* 3.0 34.4 + - - +
138B HIS* 3.7 8.5 - - - +
140B PHE* 1.3 76.6 - - - +
142B PHE* 1.3 66.2 + - - +
144B GLY* 3.0 14.5 + - - +
145B MET 4.3 4.7 + - - -
128C LYS* 5.5 11.9 - - - -
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Residues in contact with PHE 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B LEU* 4.4 10.8 - - + -
107B LYS* 3.6 35.3 + - - -
138B HIS 2.9 18.1 + - - +
139B ILE* 3.5 4.5 - - - +
140B PHE 3.2 0.2 - - - -
141B HIS* 1.3 81.3 - - - +
143B MET* 1.3 66.9 + - - +
144B GLY 3.4 0.3 + - - -
80C TRP* 3.7 33.9 - + - -
81C PHE* 3.9 15.7 - + + -
123C ASP* 4.0 20.6 - - + -
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Residues in contact with MET 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B TRP* 4.0 18.4 - - + -
98B LEU* 4.5 4.9 - - + -
106B PHE* 3.5 34.8 - - + -
107B LYS* 4.1 28.9 - - + +
110B MET* 3.9 21.3 - - + -
111B SER* 3.3 22.3 + - - -
139B ILE 3.1 11.6 + - - +
140B PHE 3.1 3.4 + - - +
142B PHE* 1.3 83.5 - - - +
144B GLY* 1.3 59.5 + - - +
145B MET* 3.5 27.4 - - + -
80C TRP* 3.9 25.6 - - + -
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Residues in contact with GLY 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B SER* 3.0 24.6 - - - +
140B PHE 2.8 3.2 + - - -
141B HIS* 3.0 15.9 + - - -
142B PHE 3.2 0.8 + - - -
143B MET* 1.3 78.1 - - - +
145B MET* 1.3 61.9 + - - +
146B SER* 3.9 2.3 + - - -
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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