Contacts of the helix formed by residues 125 - 145 (chain A) in PDB entry 2M8N
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 PRO 125 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A MET* 3.7 19.7 - - + -
123A PRO* 3.5 17.7 - - + +
124A ILE* 1.3 83.0 - - + +
126A VAL* 1.3 59.4 + - - +
127A GLY 3.2 3.6 - - - -
128A GLU* 3.0 27.2 + - + +
129A ILE* 3.0 44.3 + - + +
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Residues in contact with VAL 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A PRO* 3.7 26.9 - - + +
99A PRO* 3.8 19.1 - - + -
103A ASP 5.5 0.4 - - - +
104A ILE* 3.8 16.9 - - + +
114A GLN* 3.9 27.8 - - + +
117A TRP* 4.0 12.3 - - + -
118A MET* 4.4 3.9 - - + +
124A ILE* 2.8 36.5 + - + +
125A PRO* 1.3 70.8 - - - +
127A GLY* 1.3 65.0 + - - +
129A ILE* 3.9 8.5 - - + -
130A TYR* 3.1 26.5 + - - +
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Residues in contact with GLY 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ALA 3.4 24.7 - - - -
48A THR* 4.5 1.1 - - - -
49A PRO* 3.9 12.8 - - - +
52A LEU* 3.5 7.1 - - - +
118A MET* 4.4 9.3 - - - +
125A PRO 3.2 1.0 - - - -
126A VAL* 1.3 84.1 - - - +
128A GLU* 1.3 56.1 + - - +
131A LYS* 3.0 29.2 + - - +
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Residues in contact with GLU 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A MET* 5.0 6.9 - - + +
125A PRO* 3.0 28.5 + - + +
127A GLY* 1.3 76.3 - - - +
129A ILE* 1.3 59.2 + - + +
131A LYS* 3.4 22.4 + - - +
132A ARG* 3.0 35.7 + - + +
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Residues in contact with ILE 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A TRP* 4.2 30.3 - - + -
104A ILE* 4.0 14.1 - - + -
124A ILE* 5.5 2.2 - - + -
125A PRO* 3.0 44.0 + - + +
126A VAL* 4.1 8.3 - - + +
128A GLU* 1.3 75.7 - - + +
130A TYR* 1.3 65.8 + - - +
132A ARG* 3.3 9.8 + - + +
133A TRP* 3.2 51.5 + - + +
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Residues in contact with TYR 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A PRO* 4.0 13.7 - - + -
52A LEU* 3.4 32.8 - - + -
53A ASN* 4.5 11.1 + - + -
56A LEU* 4.2 9.2 - - - +
73A ILE* 3.6 34.2 - - + +
104A ILE* 3.3 20.1 - - + +
105A ALA* 3.5 41.7 + - + +
126A VAL 3.1 17.6 + - - +
129A ILE* 1.3 77.0 - - - +
131A LYS* 1.3 61.4 + - - +
133A TRP* 3.1 16.4 + + + -
134A ILE* 3.1 38.4 + - + +
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Residues in contact with LYS 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A PHE* 4.4 7.6 - - + -
41A SER* 4.2 13.6 + - - +
44A SER* 3.2 35.4 + - - +
45A GLU* 4.0 19.8 + - - +
46A GLY 5.2 1.6 - - - +
52A LEU* 3.6 12.9 - - + +
127A GLY 3.0 18.4 + - - +
128A GLU* 3.5 22.4 - - - +
129A ILE 3.2 0.2 - - - -
130A TYR* 1.3 76.3 - - - +
132A ARG* 1.3 58.8 + - - +
134A ILE* 3.3 7.0 + - - +
135A ILE* 2.9 51.1 + - + +
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Residues in contact with ARG 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A GLU* 3.0 27.6 + - + +
129A ILE* 3.5 10.5 - - + +
131A LYS* 1.3 78.8 - - + +
133A TRP* 1.3 65.0 + - + +
135A ILE* 3.7 18.5 - - - +
136A LEU* 2.8 47.0 + - + +
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Residues in contact with TRP 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A THR* 3.6 7.9 - - - +
73A ILE* 4.4 24.4 - - + +
76A GLU* 3.6 38.0 + - + +
77A ALA* 3.8 22.2 - - + -
80A TRP* 4.0 20.6 - + + -
101A GLY* 3.7 17.3 - - - -
104A ILE* 3.6 32.1 - - + -
105A ALA* 4.4 5.8 - - + -
129A ILE* 3.2 36.2 + - + +
130A TYR* 3.1 23.5 + + + +
132A ARG* 1.3 79.5 - - + +
134A ILE* 1.3 63.3 + - - +
136A LEU* 3.2 12.8 + - + +
137A GLY* 3.0 17.8 + - - -
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Residues in contact with ILE 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A PHE* 3.5 33.2 - - + -
52A LEU* 3.8 20.2 - - + -
56A LEU* 3.8 32.5 - - + -
69A LEU* 3.8 10.8 - - + +
73A ILE* 4.5 8.3 - - + -
130A TYR* 3.1 44.9 + - + +
131A LYS* 3.3 7.6 + - - +
133A TRP* 1.3 74.7 - - - +
135A ILE* 1.3 57.4 + - - +
137A GLY* 3.0 5.0 + - - -
138A LEU* 2.8 36.5 + - + +
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Residues in contact with ILE 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ILE* 4.2 26.5 - - + -
40A PHE* 4.2 16.4 - - + -
41A SER* 4.4 20.2 - - - -
131A LYS* 2.9 41.1 + - + +
132A ARG* 3.7 20.2 - - - +
134A ILE* 1.3 73.0 - - - +
136A LEU* 1.3 66.7 + - + +
138A LEU* 3.2 9.3 + - + +
139A ASN* 3.0 25.0 + - + +
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Residues in contact with LEU 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A THR* 3.9 7.9 - - + -
76A GLU* 3.8 36.1 - - + +
132A ARG* 2.8 52.9 + - + +
133A TRP* 3.2 10.1 + - + +
135A ILE* 1.3 76.9 - - + +
137A GLY* 1.3 61.5 + - - +
139A ASN* 3.5 7.5 + - - +
140A LYS* 3.2 22.0 + - - +
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Residues in contact with GLY 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A MET* 5.3 0.7 - - - +
69A LEU* 3.9 17.5 - - - -
72A THR* 3.6 24.2 - - - +
133A TRP 3.0 8.2 + - - -
134A ILE 3.0 9.1 + - - -
136A LEU* 1.3 73.9 - - - +
138A LEU* 1.3 57.8 + - - +
140A LYS* 3.2 5.3 + - - +
141A ILE* 2.9 30.7 + - - +
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Residues in contact with LEU 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A TRP* 5.0 7.9 - - + -
36A VAL* 4.9 14.1 - - + -
37A ILE* 3.7 26.7 - - + -
40A PHE* 3.8 42.2 - - + -
56A LEU* 6.0 1.8 - - + -
69A LEU* 3.9 15.9 - - + +
134A ILE* 2.8 28.9 + - + +
135A ILE* 3.2 7.8 + - + +
137A GLY* 1.3 72.5 - - - +
139A ASN* 1.3 57.5 + - - +
141A ILE* 3.2 14.2 + - + +
142A VAL* 2.9 33.6 + - + +
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Residues in contact with ASN 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ILE* 3.6 17.2 - - + +
135A ILE* 3.0 18.7 + - + +
136A LEU* 3.7 6.4 + - - +
138A LEU* 1.3 76.0 - - - +
140A LYS* 1.3 58.6 + - - +
142A VAL* 3.1 12.8 - - - +
143A ARG* 3.0 62.7 + - - +
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Residues in contact with LYS 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A MET* 4.0 29.9 - - + +
71A GLU* 4.9 10.8 + - - -
72A THR* 4.1 16.8 - - - +
136A LEU 3.2 12.6 + - - +
137A GLY* 3.2 10.2 + - - +
139A ASN* 1.3 78.6 - - - +
141A ILE* 1.3 58.2 + - - +
143A ARG* 3.9 5.4 - - - +
144A MET* 3.0 41.5 + - + +
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Residues in contact with ILE 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A PHE* 3.6 33.8 - - + +
65A ALA* 3.4 37.0 - - + +
68A MET* 3.7 24.0 - - + -
69A LEU* 3.8 20.4 - - + -
137A GLY 2.9 19.7 + - - +
138A LEU* 3.2 16.8 + - + +
140A LYS* 1.3 73.7 - - - +
142A VAL* 1.3 67.3 + - + +
144A MET* 3.2 5.9 + - - +
145A TYR* 3.0 22.0 + - - +
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Residues in contact with VAL 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A PHE* 3.3 32.4 - - + +
33A SER 3.7 15.9 - - - +
34A PRO* 4.3 15.7 - - + -
36A VAL* 5.6 2.5 - - + -
37A ILE* 4.8 9.9 - - + -
138A LEU* 2.9 21.4 + - + +
139A ASN* 3.1 23.8 - - - +
141A ILE* 1.3 77.0 - - + +
143A ARG* 1.3 76.5 + - + +
145A TYR* 3.2 21.2 - - - +
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Residues in contact with ARG 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A ASN* 3.0 44.7 + - - +
140A LYS* 4.0 5.4 - - - +
142A VAL* 1.3 85.4 - - + +
144A MET* 1.3 61.3 + - - +
145A TYR* 5.1 0.2 - - - +
146A SER* 4.5 4.3 + - - -
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Residues in contact with MET 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A MET* 4.3 28.5 - - + -
140A LYS* 3.0 33.0 + - + +
141A ILE* 3.2 4.9 + - - +
143A ARG* 1.3 78.6 - - - +
145A TYR* 1.3 72.9 + - - +
146A SER* 2.7 12.8 + - - +
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Residues in contact with TYR 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ALA* 5.6 2.9 - - + -
32A PHE* 3.8 42.6 - + + +
141A ILE 3.0 12.2 + - - +
142A VAL* 3.2 19.5 - - - +
144A MET* 1.3 84.0 - - - +
146A SER* 1.4 84.7 + - - +
147A PRO* 2.6 35.2 - - + +
151A LEU* 4.0 22.5 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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