Contacts of the helix formed by residues 127 - 142 (chain B) in PDB entry 3R2W
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 PHE 127 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B MET* 5.4 1.8 - - + -
116B LYS* 3.8 21.1 - - + -
117B SER* 3.8 14.4 - - - -
119B ILE* 3.5 31.9 - - + -
121B VAL* 3.3 23.6 - - + -
126B THR* 1.3 81.3 + - - +
128B LEU* 1.3 59.9 + - - +
130B LEU* 3.5 7.0 + - - +
131B THR* 3.3 23.6 + - - -
241B ILE* 3.1 34.1 - - + +
242B ASP* 3.5 27.8 - - - -
244B LEU* 4.3 13.4 - - + +
384B VAL* 3.7 33.9 - - + -
390B LEU* 5.1 0.7 - - + -
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Residues in contact with LEU 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B ASN* 5.8 2.5 - - - +
117B SER* 3.7 15.3 + - - +
118B LEU* 5.0 4.0 - - + -
126B THR* 3.1 9.7 + - + -
127B PHE* 1.3 74.3 - - - +
129B ASP* 1.3 61.5 + - - +
130B LEU 3.0 1.1 - - - -
131B THR* 2.9 7.5 + - + -
132B VAL* 2.8 34.7 + - + +
148B LEU* 5.7 0.9 - - + -
150B LEU* 3.9 26.5 - - + -
160B THR* 6.0 4.9 - - + -
163B ILE* 5.0 9.4 - - + -
164B LEU* 3.9 18.2 - - + -
167B TYR* 3.2 37.2 - - + +
174B ILE* 6.3 0.7 - - + -
241B ILE* 3.9 20.6 - - + +
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Residues in contact with ASP 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B GLU 4.8 0.7 - - - +
125B ASN* 3.7 22.1 - - + +
126B THR* 3.1 34.3 + - - +
128B LEU* 1.3 74.5 - - - +
130B LEU* 1.3 52.1 + - - +
132B VAL* 3.6 7.4 - - - +
133B GLN* 2.5 45.8 + - + +
167B TYR* 2.3 42.7 + - + -
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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
----------------------------------------------------------
121B VAL* 4.7 12.1 - - + -
122B ARG* 5.5 2.5 - - + +
125B ASN* 3.9 26.0 - - + +
126B THR 3.0 19.5 + - - +
127B PHE* 3.6 7.0 - - - +
128B LEU 3.0 0.2 - - - -
129B ASP* 1.3 75.7 - - - +
131B THR* 1.3 66.4 + - - +
133B GLN* 3.3 3.2 + - + +
134B GLN* 3.1 31.5 + - - +
244B LEU* 3.9 35.4 - - + -
400B LEU* 3.9 18.2 - - + -
403B GLY* 3.5 24.0 - - - +
405B LEU* 4.4 16.4 - - + -
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Residues in contact with THR 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B VAL* 5.3 0.4 - - + -
101B LYS* 3.3 39.4 + - + -
127B PHE 3.3 10.8 + - - -
128B LEU* 2.9 8.3 + - + -
130B LEU* 1.3 77.6 - - - +
132B VAL* 1.3 60.8 + - - +
134B GLN* 3.1 22.9 + - - +
135B ILE* 3.1 21.4 + - + +
148B LEU* 3.4 28.5 - - + -
241B ILE* 3.7 12.9 + - + +
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Residues in contact with VAL 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B LEU* 2.8 24.2 + - + +
129B ASP* 3.6 9.6 - - - +
131B THR* 1.3 72.9 - - - +
133B GLN* 1.3 69.6 + - + +
135B ILE* 4.1 6.1 - - - +
136B GLU* 3.2 29.8 + - - +
148B LEU* 3.9 21.3 - - + -
167B TYR* 3.7 49.8 - - + -
170B CYS* 6.4 0.9 - - + -
172B VAL* 4.3 12.0 - - + +
174B ILE* 4.6 11.4 - - + -
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Residues in contact with GLN 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B ASN* 3.9 24.4 + - - +
129B ASP* 2.5 37.1 + - - +
130B LEU* 3.5 4.0 - - + +
131B THR 3.2 0.2 - - - -
132B VAL* 1.3 80.7 - - - +
134B GLN* 1.3 61.3 + - - +
136B GLU* 4.0 5.4 - - - +
137B HIS* 3.3 18.0 + - - +
400B LEU* 6.0 1.7 - - - +
402B ALA* 3.6 15.1 - - - +
403B GLY* 3.2 26.3 + - - +
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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
----------------------------------------------------------
101B LYS* 5.4 3.5 + - - -
130B LEU* 3.1 19.8 + - - +
131B THR* 3.1 15.0 + - - +
133B GLN* 1.3 75.2 - - - +
135B ILE* 1.3 73.0 + - + +
137B HIS* 3.1 13.0 + - - +
138B LEU* 3.2 17.2 + - - +
244B LEU* 3.6 19.0 + - - +
246B ALA 4.6 4.0 - - - +
247B THR* 3.8 23.0 + - - +
248B VAL* 5.2 3.6 + - + +
402B ALA 3.9 6.1 - - - +
403B GLY 3.3 27.0 + - - -
404B SER* 3.4 24.0 - - - +
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Residues in contact with ILE 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B VAL* 3.9 35.7 - - + -
131B THR* 3.1 18.4 + - + +
132B VAL* 4.5 1.1 - - - +
134B GLN* 1.3 81.3 - - + +
136B GLU* 1.3 57.9 + - - +
138B LEU* 2.8 30.5 + - + +
139B ASN* 3.2 20.6 + - - +
146B VAL* 3.6 33.4 - - + +
147B PRO 5.4 1.6 - - - -
148B LEU* 4.2 20.0 - - + -
172B VAL* 3.9 15.5 - - + -
248B VAL* 4.4 13.7 - - + -
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Residues in contact with GLU 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B VAL* 3.2 22.5 + - - +
133B GLN* 4.0 6.7 - - - +
134B GLN 3.4 0.2 - - - -
135B ILE* 1.3 76.8 - - - +
137B HIS* 1.3 56.2 + - - +
139B ASN* 3.9 1.4 - - - +
140B LYS* 3.0 31.2 + - - +
170B CYS* 2.9 37.2 - - - +
171B ARG* 3.8 32.5 - - + +
172B VAL* 3.8 9.2 - - + +
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Residues in contact with HIS 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 GLN 3.3 11.5 + - - +
134B GLN* 3.1 9.3 + - - +
135B ILE 3.0 1.0 - - - -
136B GLU* 1.3 77.2 - - - +
138B LEU* 1.3 66.3 + - + +
140B LYS* 4.1 5.4 - - + -
141B THR* 2.8 50.3 + - + +
402B ALA* 3.7 32.9 + - + +
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Residues in contact with LEU 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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94B LEU* 4.4 26.2 - - + -
97B LEU* 6.2 0.2 - - + -
134B GLN 3.2 14.7 + - - +
135B ILE* 2.8 20.4 + - + +
137B HIS* 1.3 75.4 - - - +
139B ASN* 1.3 60.6 + - - +
141B THR* 2.7 26.7 + - - -
142B TYR* 2.9 33.2 + - + -
144B THR* 5.0 0.4 - - - -
146B VAL* 4.6 14.4 - - + -
248B VAL* 4.4 30.7 - - + +
250B LEU* 5.9 2.2 - - + -
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Residues in contact with ASN 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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135B ILE* 3.2 19.8 + - - +
136B GLU 4.0 2.5 - - - +
138B LEU* 1.3 78.9 - - - +
140B LYS* 1.3 61.2 + - - +
143B ASN 3.4 10.4 + - - -
144B THR* 2.8 30.7 - - - +
145B ASP* 3.2 4.9 + - - +
146B VAL* 2.8 47.9 + - - +
171B ARG* 2.9 58.6 + - - +
172B VAL* 4.2 1.8 - - - +
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Residues in contact with LYS 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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136B GLU* 3.0 22.8 + - - +
137B HIS* 4.4 7.6 - - + +
138B LEU 2.9 4.0 + - - -
139B ASN* 1.3 73.4 - - - +
141B THR* 1.3 61.4 + - + +
142B TYR 3.4 0.2 - - - -
143B ASN* 3.3 23.2 + - - -
171B ARG* 4.5 10.1 + - + +
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Residues in contact with THR 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 HIS* 2.8 51.0 + - + +
138B LEU* 2.7 8.5 + - - +
140B LYS* 1.3 76.5 - - + +
142B TYR* 1.3 80.8 + - - -
143B ASN* 3.8 2.0 - - - -
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Residues in contact with TYR 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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86B LEU* 6.1 0.2 - - - +
90B ILE 5.3 2.5 - - - -
91B SER* 3.8 27.8 - - - +
94B LEU* 4.2 15.3 - - + -
138B LEU* 2.9 30.6 + - + +
141B THR* 1.3 107.0 - - - +
143B ASN* 1.3 68.7 + - - +
144B THR* 2.8 23.8 + - + +
250B LEU* 3.8 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
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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