Contacts of the helix formed by residues 107 - 120 (chain B) in PDB entry 1MF8
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 107 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101B ASP* 4.9 1.4 + - - -
105B TYR 3.5 1.5 + - - -
106B ILE* 1.3 75.4 - - - +
108B ASN* 1.3 56.6 + - - +
109B GLY* 3.9 2.9 + - - -
110B GLU* 2.7 44.6 + - - +
111B LEU* 2.8 35.3 + - - +
136B ILE* 4.0 3.6 - - - -
146B ARG* 4.3 12.8 - - - -
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Residues in contact with ASN 108 (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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23A PHE* 4.7 5.9 - - - -
107B SER* 1.3 74.3 - - - +
109B GLY* 1.3 63.4 + - - +
112B PHE* 3.3 19.4 + - - +
129B GLN* 3.0 23.6 + - - +
132B VAL* 3.8 9.7 - - - +
133B ASP* 3.7 24.2 + - - +
136B ILE* 3.6 21.4 - - + +
145B GLY 4.6 8.2 + - - +
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Residues in contact with GLY 109 (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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107B SER* 3.2 3.2 + - - -
108B ASN* 1.3 79.0 - - - +
110B GLU* 1.3 56.7 + - - +
112B PHE* 3.2 5.1 + - - +
113B GLN* 2.5 48.6 + - - +
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Residues in contact with GLU 110 (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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98B TYR 3.7 11.4 - - - +
99B ASP* 3.4 3.6 - - - +
100B MET* 2.9 18.7 + - + +
101B ASP* 2.7 35.2 + - - +
105B TYR 3.1 11.1 - - - +
107B SER* 2.7 28.3 + - - +
109B GLY* 1.3 75.4 - - - +
111B LEU* 1.3 64.9 + - - +
113B GLN* 3.9 14.4 - - - +
114B VAL* 3.1 31.5 + - - +
403B CA 2.1 31.6 - - - -
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Residues in contact with LEU 111 (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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349A VAL* 3.4 28.0 - - + -
350A PHE* 3.1 40.4 - - + -
98B TYR* 4.3 8.7 - - + -
106B ILE* 3.2 19.0 - - + +
107B SER 2.8 20.5 + - - +
108B ASN* 4.7 0.2 - - - -
110B GLU* 1.3 73.4 - - - +
112B PHE* 1.3 61.2 + - - +
114B VAL* 4.2 3.0 - - - +
115B LEU* 2.9 41.1 + - + +
132B VAL* 3.5 31.9 - - + +
135B THR* 4.3 2.9 - - + -
136B ILE* 4.3 11.7 - - + -
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Residues in contact with PHE 112 (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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108B ASN 3.3 13.9 + - - +
109B GLY* 3.2 11.2 + - - +
110B GLU 3.1 0.6 - - - -
111B LEU* 1.3 80.6 - - - +
113B GLN* 1.3 64.9 + - + +
116B LYS* 2.9 43.1 + - + +
125B ASP* 3.5 49.1 - - + -
128B LEU* 3.1 34.2 - - + +
129B GLN* 3.3 33.4 - - + +
132B VAL* 4.1 6.5 - - + +
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Residues in contact with GLN 113 (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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100B MET* 4.0 23.5 - - + +
109B GLY* 2.5 37.8 + - - +
110B GLU* 3.9 13.4 - - - +
112B PHE* 1.3 82.1 - - + +
114B VAL* 1.3 62.7 + - - +
116B LYS* 3.4 4.6 + - - +
117B MET* 3.2 29.8 + - + +
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Residues in contact with VAL 114 (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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53B LEU* 5.3 1.3 - - + -
56B ARG* 4.7 8.7 - - + +
97B ILE* 3.3 35.0 - - + +
98B TYR* 3.7 27.8 - - + +
100B MET* 3.9 16.4 - - + -
110B GLU 3.1 18.6 + - - +
111B LEU 4.2 1.8 - - - +
113B GLN* 1.3 72.5 - - - +
115B LEU* 1.3 69.9 + - - +
117B MET* 3.0 29.9 + - - +
118B MET* 3.5 24.5 + - + +
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Residues in contact with LEU 115 (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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349A VAL* 3.7 29.4 - - + +
352A TRP* 4.7 10.5 - - + -
353A SER* 3.6 32.8 - - - +
98B TYR* 4.4 8.7 - - + -
111B LEU* 2.9 32.4 + - + +
112B PHE 3.7 2.9 - - - +
114B VAL* 1.3 77.8 - - - +
116B LYS* 1.3 56.3 - - - +
118B MET* 2.8 17.8 + - + +
119B VAL* 2.8 30.0 + - + +
128B LEU* 3.9 13.2 - - + -
132B VAL* 3.5 26.0 - - + -
8D MLE 5.1 0.8 - - + +
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Residues in contact with LYS 116 (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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112B PHE* 2.9 37.8 + - + +
113B GLN* 3.6 7.0 - - - +
115B LEU* 1.3 77.4 - - - +
117B MET* 1.3 56.9 + - - +
119B VAL* 3.5 9.4 - - + -
120B GLY* 2.7 60.7 + - - +
121B ASN* 3.1 17.2 - - - +
123B LEU 3.6 10.9 + - - -
125B ASP* 2.8 34.9 + - - +
128B LEU* 4.0 6.8 - - + +
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Residues in contact with MET 117 (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 PRO* 3.3 34.4 - - + +
53B LEU* 5.7 0.9 - - - -
55B GLN* 6.4 3.4 - - + -
56B ARG* 4.2 24.5 - - - -
100B MET* 3.6 30.1 - - + -
113B GLN* 3.2 20.0 - - + +
114B VAL* 3.0 15.4 + - - +
116B LYS* 1.3 78.3 - - + +
118B MET* 1.3 61.4 + - + +
120B GLY* 4.6 2.6 + - - -
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Residues in contact with MET 118 (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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353A SER* 3.8 19.1 - - - +
356A PHE* 3.1 52.4 - - + -
357A VAL* 3.6 25.8 - - + -
52B PRO* 4.4 4.9 - - + +
53B LEU* 3.6 29.6 - - + -
98B TYR* 4.5 1.8 - - + -
114B VAL* 3.9 29.8 - - + +
115B LEU* 2.8 18.5 + - + +
117B MET* 1.3 81.5 - - - +
119B VAL* 1.3 65.4 + - - +
5D BMT 5.1 4.0 - - - +
8D MLE 3.9 11.0 - - + +
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Residues in contact with VAL 119 (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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352A TRP* 4.3 6.3 - - + -
115B LEU 2.8 16.8 + - - +
116B LYS* 3.5 6.5 - - + -
118B MET* 1.3 76.0 - - - +
120B GLY* 1.3 77.1 + - - +
121B ASN 3.3 3.6 + - - -
122B ASN* 3.6 24.5 + - + +
123B LEU* 2.9 46.9 - - + +
128B LEU* 3.2 31.4 - - + -
5D BMT 4.5 5.0 - - + +
8D MLE 3.8 15.2 - - + +
10D MLE 5.0 3.1 - - + -
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Residues in contact with GLY 120 (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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116B LYS* 2.7 62.8 + - - +
117B MET 4.9 2.5 - - - -
118B MET 3.4 1.3 - - - -
119B VAL* 1.3 74.3 - - - +
121B ASN* 1.3 56.4 + - - -
122B ASN 3.7 0.2 - - - -
123B LEU 4.2 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
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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