Contacts of the helix formed by residues 137 - 153 (chain I) in PDB entry 2YW7
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 LEU 137 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21I LEU* 5.2 2.9 - - + -
67I GLU* 3.9 46.4 - - + +
68I VAL* 4.6 8.3 - - + -
71I ARG* 5.1 12.1 - - + -
133I VAL* 3.0 27.1 - - + +
134I SER* 3.4 11.0 - - - +
136I ASP* 1.3 80.4 - - - +
138I LEU* 1.3 72.9 - - + +
139I ILE* 3.0 3.0 + - - +
140I ALA* 3.1 7.6 + - + +
141I HIS* 2.9 49.1 + - + +
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Residues in contact with LEU 138 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20I LEU 5.8 1.1 - - - +
21I LEU* 3.9 26.0 - - + -
24I GLN* 4.2 15.9 - - + -
28I TYR* 4.2 7.4 - - - +
68I VAL* 4.6 2.9 - - + -
120I THR* 3.3 10.6 - - + +
123I SER* 4.3 15.3 - - - -
124I ILE* 3.3 26.7 - - + -
127I LEU* 3.9 25.8 - - + -
134I SER 3.1 13.2 + - - +
137I LEU* 1.3 93.3 - - + +
139I ILE* 1.3 51.7 + - - +
141I HIS* 3.8 14.8 - - - +
142I ALA* 2.6 36.0 + - - +
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Residues in contact with ILE 139 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124I ILE* 3.6 20.2 - - + +
134I SER 4.7 0.4 + - - -
135I GLN* 4.6 2.9 - - + -
136I ASP* 3.7 35.0 - - - +
137I LEU 3.8 0.4 - - - +
138I LEU* 1.3 73.5 - - - +
140I ALA* 1.3 65.0 + - + +
141I HIS 3.0 1.1 - - - -
142I ALA* 2.7 8.3 + - + +
143I GLY* 2.4 41.6 + - - +
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Residues in contact with ALA 140 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64I TYR* 5.2 0.4 - - - -
136I ASP 4.5 9.6 - - - +
137I LEU* 3.1 10.8 + - - +
139I ILE* 1.3 81.4 - - + +
141I HIS* 1.3 65.7 + - + +
143I GLY* 3.4 2.8 + - - +
144I GLU* 3.1 34.9 + - + +
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Residues in contact with HIS 141 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28I TYR* 2.8 31.2 + + - +
64I TYR* 3.4 56.8 - + + +
67I GLU* 3.1 24.5 + - + -
68I VAL* 4.8 1.1 - - + -
120I THR* 5.1 0.2 - - + -
137I LEU* 2.9 40.2 + - + +
138I LEU* 3.4 14.9 - - + +
139I ILE 2.9 0.4 + - - -
140I ALA* 1.3 74.5 - - + +
142I ALA* 1.3 56.6 + - - +
143I GLY 3.0 0.9 - - - -
144I GLU* 2.9 5.5 + - - +
145I LEU* 2.7 42.0 + - + +
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Residues in contact with ALA 142 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117I ILE* 5.3 4.5 - - + +
120I THR* 3.8 16.6 - - + -
121I ARG* 5.0 12.8 - - + +
124I ILE* 4.1 10.3 - - + -
138I LEU 2.6 22.2 + - - +
139I ILE* 2.7 8.6 + - + +
141I HIS* 1.3 73.3 - - - +
143I GLY* 1.3 53.8 + - - +
145I LEU* 3.8 13.4 - - - +
146I GLU* 2.7 40.8 + - + +
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Residues in contact with GLY 143 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139I ILE* 2.4 25.5 + - - +
140I ALA* 3.6 3.4 - - - -
141I HIS 2.9 0.8 + - - -
142I ALA* 1.3 72.3 - - - +
144I GLU* 1.3 58.6 + - - -
146I GLU* 3.6 8.4 - - - +
147I LYS* 2.8 34.0 + - - +
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Residues in contact with GLU 144 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57I GLN* 4.4 6.0 + - - +
60I LEU* 5.1 10.3 - - + -
64I TYR* 3.2 24.9 - - - +
140I ALA* 3.1 18.4 + - + +
141I HIS 2.9 4.8 + - - -
143I GLY* 1.3 73.6 - - - -
145I LEU* 1.3 59.5 + - - +
147I LYS* 3.3 17.3 - - - +
148I PHE* 3.1 24.3 + - - +
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Residues in contact with LEU 145 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28I TYR* 4.3 16.4 - - + -
31I LEU* 4.6 9.2 - - + -
57I GLN* 4.7 4.7 - - - +
61I VAL* 5.2 2.0 - - + -
64I TYR* 4.2 15.3 - - + -
113I TYR* 3.6 38.4 - - + +
116I VAL* 4.5 17.9 - - + +
117I ILE* 4.5 7.2 - - + -
120I THR* 4.1 16.6 - - + +
141I HIS* 2.7 38.7 + - + +
142I ALA* 3.7 10.5 - - - +
144I GLU* 1.3 68.5 - - - +
146I GLU* 1.3 59.2 + - - +
147I LYS 3.0 0.9 - - - -
148I PHE* 2.7 25.4 + - - +
149I GLN 3.0 9.7 + - - -
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Residues in contact with GLU 146 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117I ILE* 3.6 20.1 - - + +
121I ARG* 2.7 36.1 + - - +
142I ALA* 2.7 26.3 + - - +
143I GLY* 3.6 6.5 - - - +
145I LEU* 1.3 73.1 - - - +
147I LYS* 1.3 61.9 + - - +
149I GLN* 3.4 15.3 + - - +
150I TRP* 3.6 6.8 + - - +
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Residues in contact with LYS 147 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143I GLY 2.8 17.7 + - - +
144I GLU* 3.3 22.4 - - + +
146I GLU* 1.3 72.3 - - - +
148I PHE* 1.3 68.9 + - - +
150I TRP* 3.1 32.6 + - - +
151I PHE* 3.2 47.1 + - - +
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Residues in contact with PHE 148 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35I LEU* 5.3 3.4 - - + -
53I MET* 3.6 42.0 - - + -
54I ILE* 4.8 5.8 - - + -
57I GLN* 3.2 54.1 - - + +
109I LEU* 4.1 19.1 - - + -
113I TYR* 3.2 37.7 - + + -
144I GLU 3.1 4.9 + - - +
145I LEU 2.7 14.8 + - - +
147I LYS* 1.3 77.4 - - - +
149I GLN* 1.3 62.0 + - - +
151I PHE* 2.9 33.9 + + + +
152I VAL* 3.2 15.7 + - + +
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Residues in contact with GLN 149 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110I ASP* 2.6 30.4 + - - +
113I TYR* 3.6 24.0 - - + -
114I ASN* 2.9 25.8 + - - +
117I ILE* 2.8 32.5 - - + +
145I LEU 3.0 5.8 + - - +
146I GLU* 3.5 11.3 - - - +
147I LYS 3.2 0.2 - - - -
148I PHE* 1.3 77.8 - - - +
150I TRP* 1.3 59.9 + - - +
152I VAL* 3.2 24.0 - - - +
153I ARG* 3.2 32.8 + - - +
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Residues in contact with TRP 150 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146I GLU 3.6 5.8 + - - +
147I LYS* 3.1 28.0 + - - +
149I GLN* 1.3 74.2 - - - +
151I PHE* 1.3 57.3 + + - +
152I VAL 2.8 16.2 + - - -
153I ARG* 3.5 40.4 + - + +
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Residues in contact with PHE 151 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53I MET* 3.8 45.4 - - + +
147I LYS* 3.2 33.4 + - - +
148I PHE* 2.9 25.2 + + + +
150I TRP* 1.3 79.0 - + - +
152I VAL* 1.3 62.6 + - - +
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Residues in contact with VAL 152 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53I MET* 4.6 8.8 - - + +
106I LEU* 3.3 56.8 - - + +
109I LEU* 4.9 9.4 - - + +
110I ASP* 4.7 11.7 - - + +
113I TYR* 5.8 0.4 - - + -
148I PHE* 3.3 28.7 - - + +
149I GLN* 3.2 22.2 - - + +
150I TRP 2.8 1.6 + - - -
151I PHE* 1.3 83.0 - - - +
153I ARG* 1.3 75.5 + - - +
154I ALA* 3.4 2.8 + - - -
155I HIS 4.6 0.2 + - - -
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Residues in contact with ARG 153 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110I ASP* 3.6 23.6 + - - -
114I ASN* 5.2 0.8 + - - +
149I GLN* 3.2 43.0 + - - +
150I TRP* 3.9 35.5 - - + +
152I VAL* 1.3 85.0 - - - +
154I ALA* 1.3 53.5 + - - +
155I HIS* 2.7 21.4 + - - +
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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