Contacts of the helix formed by residues 125 - 145 (chain B) in PDB entry 2M8L
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B MET* 4.7 12.3 - - + -
123B PRO* 3.5 21.1 - - + +
124B ILE* 1.3 81.4 - - + +
126B VAL* 1.3 59.0 + - - +
127B GLY 3.2 3.8 - - - -
128B GLU* 3.0 27.9 + - + +
129B ILE* 3.0 44.0 + - + +
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Residues in contact with VAL 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B PRO* 3.7 25.6 - - + +
99B PRO* 3.8 18.2 - - + -
104B ILE* 3.8 15.4 - - + +
114B GLN* 3.9 32.3 - - - +
117B TRP* 3.9 11.9 - - + -
118B MET* 4.9 3.5 - - + +
124B ILE* 2.8 37.4 + - + +
125B PRO* 1.3 70.4 - - - +
127B GLY* 1.3 65.1 + - - +
129B ILE* 3.8 9.4 - - + -
130B TYR* 3.1 26.3 + - - +
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Residues in contact with GLY 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ALA 3.4 25.1 - - - -
48B THR* 4.5 1.6 - - - -
49B PRO* 3.9 13.0 - - - +
52B LEU* 3.5 6.7 - - - +
118B MET* 5.3 7.3 - - - +
125B PRO 3.2 1.0 - - - -
126B VAL* 1.3 83.6 - - - +
128B GLU* 1.3 56.7 + - - +
131B LYS* 3.0 31.8 + - - +
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Residues in contact with GLU 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B PRO* 3.0 28.7 + - + +
127B GLY* 1.3 76.1 - - - +
129B ILE* 1.3 60.2 + - + +
131B LYS* 3.4 14.2 + - + +
132B ARG* 3.0 27.1 + - + +
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Residues in contact with ILE 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B TRP* 4.2 29.8 - - + -
104B ILE* 4.0 13.2 - - + -
124B ILE* 5.4 2.7 - - + -
125B PRO* 3.0 43.5 + - + +
126B VAL* 4.1 7.6 - - + +
128B GLU* 1.3 76.1 - - + +
130B TYR* 1.3 66.3 + - - +
132B ARG* 3.3 8.8 + - + +
133B TRP* 3.2 53.1 + - + +
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Residues in contact with TYR 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B PRO* 4.0 13.9 - - + -
52B LEU* 3.4 32.3 - - + -
53B ASN* 4.5 10.9 + - + +
56B LEU* 4.2 8.7 - - - +
73B ILE* 3.6 34.5 - - + +
104B ILE* 3.3 20.8 - - + +
105B ALA* 3.5 43.7 + - + +
126B VAL 3.1 18.8 + - - +
129B ILE* 1.3 75.9 - - - +
131B LYS* 1.3 62.8 + - - +
133B TRP* 3.1 15.7 + + - +
134B ILE* 3.1 37.6 + - + +
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Residues in contact with LYS 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B PHE* 4.3 8.1 - - + -
41B SER* 3.9 11.2 + - - +
44B SER* 2.9 53.3 + - - +
45B GLU* 3.6 10.1 - - - +
46B GLY 4.2 3.6 - - - +
47B ALA* 5.2 2.5 - - - +
52B LEU* 3.6 13.4 - - + +
127B GLY 3.0 20.8 + - - +
128B GLU* 3.5 14.5 - - + +
129B ILE 3.2 0.2 - - - -
130B TYR* 1.3 75.9 - - - +
132B ARG* 1.3 57.2 + - - +
134B ILE* 3.3 6.7 + - - +
135B ILE* 2.9 50.3 + - + +
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Residues in contact with ARG 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B GLU* 3.0 13.1 + - + +
129B ILE* 3.5 12.1 - - - +
131B LYS* 1.3 77.6 - - - +
133B TRP* 1.3 68.9 + - + +
135B ILE* 3.7 9.5 - - + +
136B LEU* 2.9 45.9 + - + +
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Residues in contact with TRP 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B THR* 3.6 7.8 - - - +
73B ILE* 4.4 23.9 - - + +
76B GLU* 3.6 36.7 - - + +
77B ALA* 3.8 23.1 - - + -
80B TRP* 4.0 19.7 - + + -
101B GLY* 3.7 16.6 - - - -
104B ILE* 3.6 32.8 - - + -
105B ALA* 4.4 5.6 - - + -
129B ILE* 3.2 35.8 + - + +
130B TYR* 3.1 22.9 + + + +
132B ARG* 1.3 83.4 - - + +
134B ILE* 1.3 63.5 + - - +
136B LEU* 3.2 14.0 + - + +
137B GLY* 3.0 17.7 + - - -
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Residues in contact with ILE 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B PHE* 3.5 31.9 - - + -
52B LEU* 3.8 20.4 - - + -
56B LEU* 3.7 27.4 - - + -
69B LEU* 3.6 21.1 - - + +
73B ILE* 4.5 7.2 - - + -
130B TYR* 3.1 46.0 + - + +
131B LYS* 3.6 6.5 - - - +
133B TRP* 1.3 75.1 - - - +
135B ILE* 1.3 57.3 + - - +
137B GLY* 3.0 4.7 + - - -
138B LEU* 2.8 33.6 + - + +
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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
----------------------------------------------------------
37B ILE* 4.1 24.5 - - + -
40B PHE* 4.2 16.6 - - + -
41B SER* 4.4 19.7 - - - -
131B LYS* 2.9 38.7 + - + +
132B ARG* 3.7 9.0 - - + +
134B ILE* 1.3 73.1 - - - +
136B LEU* 1.3 66.5 + - + +
138B LEU* 3.2 9.7 + - + +
139B ASN* 3.0 24.9 + - + +
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Residues in contact with LEU 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B THR* 3.9 8.3 - - + -
76B GLU* 3.5 35.7 - - + +
132B ARG* 2.9 44.0 + - + +
133B TRP* 3.3 11.9 - - + +
135B ILE* 1.3 77.4 - - + +
137B GLY* 1.3 61.2 + - - +
139B ASN* 3.5 6.4 + - - +
140B LYS* 3.2 27.5 + - + +
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Residues in contact with GLY 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B MET* 3.8 2.9 - - - +
69B LEU* 4.3 8.5 - - - -
72B THR* 3.6 25.7 - - - +
133B TRP 3.0 7.6 + - - -
134B ILE 3.0 8.7 + - - -
136B LEU* 1.3 74.7 - - - +
138B LEU* 1.3 59.1 + - - +
140B LYS* 3.2 4.7 + - - +
141B ILE* 2.9 36.6 + - - +
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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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23B TRP* 5.0 7.6 - - + -
36B VAL* 4.9 13.0 - - + -
37B ILE* 3.6 29.2 - - + -
40B PHE* 3.8 42.2 - - + -
56B LEU* 6.0 3.4 - - + -
69B LEU* 4.5 11.0 - - + -
134B ILE* 2.8 26.9 + - + +
135B ILE* 3.2 7.8 + - + +
137B GLY* 1.3 72.3 - - - +
139B ASN* 1.3 58.8 + - - +
141B ILE* 3.2 15.7 + - + +
142B VAL* 2.9 32.9 + - - +
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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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37B ILE* 4.4 7.9 - - + +
135B ILE* 3.0 19.8 + - + +
136B LEU* 3.7 6.6 + - - +
138B LEU* 1.3 75.2 - - - +
140B LYS* 1.3 61.8 + - - +
142B VAL* 3.1 15.5 - - - +
143B ARG* 3.0 43.8 + - - +
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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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68B MET* 3.6 34.1 - - + +
71B GLU* 4.6 4.8 + - - -
72B THR* 4.5 7.8 + - + +
136B LEU* 3.2 17.0 + - + +
137B GLY 3.2 9.3 + - - +
139B ASN* 1.3 79.1 - - - +
141B ILE* 1.3 58.3 + - - +
143B ARG* 3.1 36.3 - - - +
144B MET* 2.7 49.3 + - + +
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Residues in contact with ILE 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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32B PHE* 3.6 32.5 - - + -
65B ALA* 3.4 38.1 - - + +
68B MET* 3.7 22.7 - - + -
69B LEU* 4.5 7.9 - - + +
137B GLY 2.9 24.6 + - - +
138B LEU* 3.2 21.5 + - + +
140B LYS* 1.3 73.7 - - - +
142B VAL* 1.3 68.7 + - + +
144B MET* 3.2 5.4 + - - +
145B TYR* 3.0 25.3 + - + +
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Residues in contact with VAL 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B PHE* 3.3 31.7 - - + +
33B SER 3.8 15.3 - - - +
34B PRO* 4.3 14.6 - - + -
36B VAL* 5.6 0.7 - - + -
37B ILE* 3.8 15.3 - - + -
138B LEU 2.9 19.2 + - - +
139B ASN* 3.1 23.8 - - - +
141B ILE* 1.3 76.7 - - + +
143B ARG* 1.3 77.9 + - + +
145B TYR 3.2 20.0 + - - +
146B SER* 4.8 1.2 - - - -
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Residues in contact with ARG 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A LYS* 5.8 6.1 - - - +
139B ASN* 3.0 28.2 + - - +
140B LYS* 3.1 36.9 - - - +
142B VAL* 1.3 85.0 - - + +
144B MET* 1.3 84.6 + - - +
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Residues in contact with MET 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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68B MET* 5.5 7.6 - - + -
140B LYS* 2.7 53.4 + - + +
141B ILE* 3.2 4.9 + - - +
143B ARG* 1.3 117.4 - - - +
145B TYR* 1.3 65.8 + - + +
146B SER 4.1 0.3 + - - -
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Residues in contact with TYR 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B PHE* 3.8 34.7 - + + +
141B ILE* 3.0 16.2 + - + +
142B VAL* 3.2 13.4 + - - +
144B MET* 1.3 85.0 - - + +
146B SER* 1.3 90.4 + - - +
147B PRO* 4.3 1.6 - - - +
148B THR* 5.7 3.6 - - - -
152B ASP* 2.8 35.1 + - - -
153B ILE* 6.0 1.2 - - - +
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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
------------------------------------------------------------
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