Contacts of the helix formed by residues 121 - 138 (chain B) in PDB entry 4M6W
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 SER 121 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60B TYR* 4.5 1.1 - - - -
92B GLU* 5.0 2.5 - - - -
119B VAL* 2.8 23.0 - - - +
120B ALA* 1.3 80.5 - - - +
122B GLN* 1.3 61.1 + - - +
123B MET* 3.1 15.4 + - - +
124B GLU* 3.0 31.1 + - - +
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Residues in contact with GLN 122 (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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25B TRP* 4.2 14.5 - - - -
28B SER* 4.0 7.1 - - - -
29B GLN* 3.3 27.6 + - + +
30B LEU* 3.0 38.5 + - + +
60B TYR* 3.2 22.3 + - - +
62B THR* 6.2 0.6 - - - +
92B GLU* 3.9 14.7 + - - +
121B SER* 1.3 70.7 - - - +
123B MET* 1.3 62.2 + - - +
124B GLU 3.3 0.9 - - - -
125B ALA* 3.7 4.5 - - - -
126B SER* 3.1 23.9 + - - -
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Residues in contact with MET 123 (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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29B GLN* 3.6 34.7 - - + +
33B GLU* 3.7 19.2 - - + +
121B SER* 3.1 13.2 - - - +
122B GLN* 1.3 81.4 - - - +
124B GLU* 1.3 60.5 + - - +
126B SER* 3.4 18.8 - - - -
127B CYS* 3.8 10.4 + - - -
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Residues in contact with GLU 124 (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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1916A LYS* 5.7 7.8 - - - +
1919A ASP* 4.7 2.8 - - - +
118B PRO 4.9 0.5 - - - +
119B VAL* 3.6 14.0 - - + +
120B ALA* 2.8 35.9 + - + +
121B SER* 3.0 24.0 + - - +
122B GLN 3.3 0.2 - - - -
123B MET* 1.3 74.4 - - - +
125B ALA* 1.3 62.9 + - - +
126B SER 3.2 0.4 - - - -
127B CYS* 3.4 8.9 + - - +
128B LEU* 3.1 21.5 + - - +
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Residues in contact with ALA 125 (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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30B LEU* 3.8 7.9 - - + -
60B TYR* 3.7 32.1 - - + -
90B VAL* 4.6 4.7 - - + -
119B VAL* 3.9 21.0 - - + +
121B SER 3.5 2.8 + - - -
122B GLN* 3.7 10.3 - - - +
123B MET 3.4 0.4 - - - -
124B GLU* 1.3 75.7 - - - +
126B SER* 1.3 60.4 + - - +
128B LEU* 4.1 4.0 - - - -
129B VAL* 2.9 37.7 + - + +
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Residues in contact with SER 126 (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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29B GLN 4.0 0.2 + - - -
30B LEU* 3.5 25.3 + - - +
33B GLU* 3.4 36.5 - - - +
34B MET* 4.4 6.4 - - - +
122B GLN 3.1 14.4 + - - -
123B MET* 3.4 13.0 + - - -
124B GLU 3.2 0.2 - - - -
125B ALA* 1.3 79.1 - - - +
127B CYS* 1.3 64.5 + - - +
129B VAL* 3.8 1.7 - - - +
130B ILE* 3.0 31.1 + - - +
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Residues in contact with CYS 127 (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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1919A ASP* 4.5 10.4 - - - +
33B GLU* 5.8 4.7 - - - -
123B MET 3.8 9.1 + - - -
124B GLU* 3.4 10.3 + - - +
126B SER* 1.3 79.9 - - - +
128B LEU* 1.3 61.8 + - - +
130B ILE* 3.5 12.9 + - - +
131B GLN* 3.1 24.4 + - - +
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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
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1919A ASP* 4.0 34.4 + - + +
1922A LEU* 5.1 11.9 - - + -
1923A THR* 5.0 8.1 - - + -
1926A ILE* 6.1 0.7 - - + -
90B VAL* 4.1 11.9 - - + -
117B LEU* 3.9 39.3 - - + -
118B PRO 5.0 1.1 - - - +
119B VAL* 3.9 24.5 - - + -
124B GLU 3.1 16.2 + - - +
125B ALA* 3.6 5.2 - - - +
126B SER 3.2 0.2 - - - -
127B CYS* 1.3 74.1 - - - +
129B VAL* 1.3 62.3 + - + +
131B GLN* 3.3 4.4 + - - +
132B LEU* 2.8 33.4 + - + +
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Residues in contact with VAL 129 (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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19B ILE* 5.0 7.9 - - + -
30B LEU* 4.8 7.9 - - + -
34B MET* 3.9 23.6 - - + -
38B ILE* 5.2 0.9 - - + -
50B PHE* 5.1 11.0 - - + -
52B LEU* 4.9 1.6 - - + -
58B ILE* 3.9 32.8 - - + -
60B TYR* 6.2 2.0 - - + -
90B VAL* 5.4 5.4 - - + -
125B ALA* 2.9 30.0 + - + +
126B SER 3.9 2.0 - - - +
128B LEU* 1.3 71.8 - - + +
130B ILE* 1.3 66.0 + - - +
132B LEU* 3.4 9.4 - - + +
133B VAL* 2.9 34.9 + - + +
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Residues in contact with ILE 130 (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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33B GLU* 4.2 18.4 - - + +
34B MET* 4.3 9.6 - - + -
37B LYS* 4.1 38.8 - - + -
38B ILE* 3.7 26.5 - - + -
126B SER* 3.0 27.9 + - - +
127B CYS* 3.6 11.9 - - - +
128B LEU 3.2 0.2 - - - -
129B VAL* 1.3 75.2 - - - +
131B GLN* 1.3 62.3 + - + +
133B VAL* 3.1 5.9 + - - +
134B GLN* 2.9 45.2 + - + +
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Residues in contact with GLN 131 (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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1919A ASP* 4.2 9.0 - - + +
1920A SER* 3.9 39.7 - - - +
1923A THR* 3.8 11.1 + - + +
127B CYS 3.1 15.0 + - - +
128B LEU 3.9 2.9 - - - +
130B ILE* 1.3 81.9 - - + +
132B LEU* 1.3 57.1 + - - +
134B GLN* 3.6 21.4 - - - +
135B GLU* 3.0 30.7 + - - +
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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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1923A THR* 3.9 21.7 - - + +
1926A ILE* 4.7 16.6 - - + -
52B LEU* 4.1 13.7 - - + +
58B ILE* 3.9 17.7 - - + -
88B ILE* 3.7 33.4 - - + -
90B VAL* 5.1 2.2 - - + -
117B LEU* 4.2 19.3 - - + -
128B LEU* 2.8 24.7 + - + +
129B VAL* 3.4 9.9 - - + +
131B GLN* 1.3 75.2 - - - +
133B VAL* 1.3 62.5 + - - +
135B GLU* 3.6 7.2 - - + +
136B GLN* 3.2 22.3 + - - +
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Residues in contact with VAL 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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18B HIS* 3.8 20.6 - - + +
19B ILE* 3.7 26.9 - - + -
38B ILE* 4.0 16.2 - - + -
52B LEU* 3.8 20.2 - - + -
129B VAL* 2.9 22.7 + - + +
130B ILE 3.5 7.2 - - - +
132B LEU* 1.3 73.1 - - - +
134B GLN* 1.3 61.4 + - - +
136B GLN* 2.9 6.0 + - - +
137B THR* 2.8 54.2 + - + +
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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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18B HIS* 5.1 6.3 - - - -
37B LYS* 5.2 4.9 + - - +
38B ILE* 4.9 7.7 - - - +
130B ILE* 2.9 36.6 + - + +
131B GLN* 3.6 26.7 - - - +
133B VAL* 1.3 83.8 - - - +
135B GLU* 1.3 62.6 + - - +
137B THR* 3.4 8.2 + - - -
138B LYS* 3.2 29.1 + - - +
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Residues in contact with GLU 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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1923A THR* 3.6 36.8 + - - +
1924A THR* 4.1 9.7 + - - +
1927A GLY* 4.3 9.7 - - - -
131B GLN* 3.0 22.7 + - - +
132B LEU* 3.6 9.2 - - + +
133B VAL 3.2 0.2 - - - -
134B GLN* 1.3 77.5 - - - +
136B GLN* 1.3 63.4 + - + +
138B LYS* 3.7 13.4 + - - +
139B GLU 5.4 0.3 - - - +
143B ASN* 2.8 40.2 + - - +
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Residues in contact with GLN 136 (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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52B LEU* 4.3 27.3 + - + +
53B SER* 2.7 36.1 + - - -
55B ARG* 4.3 9.6 - - - +
56B CYS* 3.9 11.7 - - - +
132B LEU 3.2 9.9 + - - +
133B VAL* 2.9 11.4 + - - +
135B GLU* 1.3 82.2 - - - +
137B THR* 1.3 66.9 + - + +
138B LYS 3.4 7.8 - - - +
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Residues in contact with THR 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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18B HIS* 4.2 18.5 - - + +
19B ILE* 5.9 1.3 - - + -
52B LEU 5.9 2.9 - - - +
133B VAL* 2.8 41.2 + - + +
134B GLN* 3.4 14.2 + - - -
136B GLN* 1.3 75.0 - - + +
138B LYS* 1.3 67.3 + - - +
139B GLU* 3.8 7.8 + - - +
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Residues in contact with LYS 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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134B GLN 3.2 17.3 + - - +
135B GLU* 3.7 9.7 - - - +
136B GLN 3.4 9.2 - - - +
137B THR* 1.3 84.9 + - - +
139B GLU* 1.3 99.9 + - - +
140B PRO* 4.5 0.9 - - - +
142B LYS* 3.8 28.9 - - + -
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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