Contacts of the helix formed by residues 99 - 114 (chain F) in PDB entry 3MX4
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 99 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43F PHE 3.2 23.6 - - - -
44F GLN* 3.7 9.6 - - - +
45F GLY 3.7 7.2 - - - +
97F ALA 3.7 1.3 + - - -
98F GLY* 1.3 75.2 - - - -
100F GLU* 1.3 64.7 + - - +
101F LEU 3.2 3.5 + - - -
102F SER* 3.5 3.1 + - - -
103F ASN* 3.0 39.0 + - - -
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Residues in contact with GLU 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45F GLY* 3.5 9.6 + - - +
46F ALA* 4.0 11.9 + - + +
80F ALA* 3.7 7.0 - - + +
81F VAL 3.4 24.9 - - - +
82F PRO* 4.1 11.2 - - + +
83F ALA* 3.5 22.3 + - - +
98F GLY* 3.2 26.9 - - - +
99F SER* 1.3 80.4 + - - +
101F LEU* 1.3 57.8 + - - +
103F ASN* 3.8 6.6 - - - +
104F ARG* 2.9 39.9 + - + +
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Residues in contact with LEU 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43F PHE* 4.0 7.0 - - + -
45F GLY 2.9 21.6 + - - +
46F ALA 4.0 4.5 - - - -
47F GLY* 3.7 22.4 - - - +
48F VAL 4.0 2.9 - - - +
49F TYR* 3.5 32.5 - - + -
80F ALA* 3.6 8.3 - - + +
100F GLU* 1.3 73.7 - - - +
102F SER* 1.3 65.3 + - - +
104F ARG* 3.5 0.9 + - - +
105F ILE* 3.2 32.8 + - + +
127F PHE* 3.9 17.0 - - + -
128F VAL 3.6 21.1 - - - +
129F ILE* 3.8 23.3 - - + -
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Residues in contact with SER 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39F PRO* 6.0 1.7 - - - +
41F GLU 4.6 0.3 + - - -
42F ARG* 3.6 22.2 - - - +
43F PHE* 3.3 50.0 - - - -
45F GLY 4.4 0.6 + - - -
99F SER* 3.5 5.8 + - - -
101F LEU* 1.3 77.7 - - - +
103F ASN* 1.3 67.1 + - - +
105F ILE* 3.5 3.9 + - - +
106F ARG* 3.0 38.1 + - - +
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Residues in contact with ASN 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42F ARG* 4.7 15.4 - - - +
99F SER* 3.0 36.8 + - - +
100F GLU* 3.8 6.5 - - - +
101F LEU 3.2 0.4 - - - -
102F SER* 1.3 86.4 + - - +
104F ARG* 1.3 64.7 + - + +
106F ARG* 3.2 8.7 + - - +
107F GLU* 2.8 24.7 + - - +
110F ARG* 4.6 2.9 + - - +
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Residues in contact with ARG 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49F TYR* 3.9 16.8 + - + +
76F TYR* 4.7 5.1 + - - -
79F LYS 2.7 29.9 + - - -
80F ALA* 3.7 11.3 - - + +
100F GLU* 2.9 26.1 + - + +
101F LEU 4.2 2.7 - - - +
103F ASN* 1.3 75.6 - - - +
105F ILE* 1.3 58.7 + - - +
107F GLU* 3.3 21.6 + - - +
108F HIS* 2.9 59.9 + - - -
161F GLY* 4.5 12.9 + - - -
163F HIS* 4.7 10.8 + - - -
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Residues in contact with ILE 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F LEU* 3.2 31.6 - - + +
38F PRO* 4.4 0.9 - - + -
39F PRO* 3.9 21.1 - - + -
43F PHE* 4.4 8.7 - - + -
49F TYR* 3.9 29.2 - - + -
51F LEU* 5.1 2.9 - - + -
101F LEU* 3.2 26.8 + - + +
102F SER* 4.0 3.1 - - - +
104F ARG* 1.3 75.5 - - - +
106F ARG* 1.3 64.2 + - - +
108F HIS* 3.0 8.4 + - - +
109F GLY* 2.9 20.8 + - - -
125F CYS* 4.4 7.4 - - - -
127F PHE* 4.0 35.4 - - + -
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Residues in contact with ARG 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38F PRO* 3.9 36.0 - - + +
39F PRO* 5.2 4.3 - - + -
41F GLU 5.9 0.7 - - - -
42F ARG* 3.2 45.9 - - - +
102F SER* 3.0 36.6 + - - +
103F ASN* 3.8 8.5 - - - +
105F ILE* 1.3 73.7 - - - +
107F GLU* 1.3 58.6 + - - +
109F GLY* 3.2 2.4 + - - -
110F ARG* 2.9 47.7 + - - +
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Residues in contact with GLU 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103F ASN 2.8 17.1 + - - +
104F ARG* 3.5 20.2 + - - +
106F ARG* 1.3 74.5 - - - +
108F HIS* 1.3 71.2 + - + +
110F ARG* 3.0 34.0 + - - +
111F ASN* 3.2 28.9 + - - +
162F ASN 5.3 0.9 - - - +
163F HIS* 3.7 33.6 + - - -
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Residues in contact with HIS 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F LEU* 4.9 1.8 - - + -
49F TYR* 2.7 41.4 + + - -
51F LEU* 4.4 9.4 - - + -
76F TYR* 3.9 7.1 + + - -
104F ARG* 2.9 45.0 + - - -
105F ILE* 3.0 6.9 + - - +
107F GLU* 1.3 80.0 - - + +
109F GLY* 1.3 63.3 + - - +
110F ARG 3.2 0.2 + - - -
111F ASN* 3.4 8.9 + - - +
112F ILE* 3.1 28.1 + - - +
160F PHE* 3.3 40.3 + + + -
161F GLY* 4.0 21.8 - - - -
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Residues in contact with GLY 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F LEU* 4.1 12.0 - - - +
38F PRO* 5.3 4.5 - - - -
105F ILE 2.9 13.6 + - - -
106F ARG* 3.6 4.9 - - - -
108F HIS* 1.3 77.8 - - - +
110F ARG* 1.3 60.8 + - - +
112F ILE* 3.3 1.6 + - - +
113F ALA* 3.2 22.7 + - - +
120F LEU* 3.8 29.1 - - - +
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Residues in contact with ARG 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103F ASN* 4.6 2.8 + - - +
106F ARG* 2.9 29.1 + - - +
107F GLU* 3.0 43.4 + - - +
109F GLY* 1.3 77.5 - - - +
111F ASN* 1.3 59.2 + - - +
113F ALA* 3.3 10.2 + - + +
114F LYS* 3.1 33.0 + - + +
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Residues in contact with ASN 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107F GLU* 3.2 29.0 + - - +
108F HIS* 3.7 13.5 + - - +
110F ARG* 1.3 75.6 - - - +
112F ILE* 1.3 65.5 + - - +
114F LYS* 3.2 25.7 + - - +
115F THR* 3.5 14.2 + - - +
160F PHE* 4.3 16.3 + - + -
162F ASN 5.0 3.0 + - - -
177F TRP* 3.9 5.9 - - + -
184F ARG* 3.7 45.3 + - + +
186F TRP* 5.8 0.3 + - - -
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Residues in contact with ILE 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F LEU* 3.7 29.4 - - + -
51F LEU* 4.9 1.6 - - + -
108F HIS 3.1 10.9 + - - +
109F GLY 3.3 6.3 + - - +
111F ASN* 1.3 76.2 - - - +
113F ALA* 1.3 58.7 + - - +
115F THR* 2.6 36.8 + - - -
118F LEU* 3.7 13.5 - - + +
120F LEU* 3.8 24.0 - - + +
123F PHE* 3.7 44.6 - - + -
153F TRP* 4.5 7.4 - - + -
160F PHE* 4.2 22.7 - - + -
177F TRP* 4.9 0.9 - - + -
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Residues in contact with ALA 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109F GLY 3.2 10.5 + - - +
110F ARG* 3.3 13.9 - - + +
111F ASN 3.2 0.2 - - - -
112F ILE* 1.3 82.1 - - - +
114F LYS* 1.3 60.6 + - + +
115F THR 3.3 7.8 + - - +
118F LEU 5.2 2.6 - - - +
120F LEU* 4.4 18.4 - - + +
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Residues in contact with LYS 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110F ARG* 3.1 22.1 + - + +
111F ASN* 3.8 21.3 + - - +
112F ILE 3.2 0.8 - - - -
113F ALA* 1.3 74.1 - - - +
115F THR* 1.3 62.6 + - - +
182F PRO 4.3 0.2 - - - -
183F GLY 3.5 28.6 + - - +
184F ARG* 4.3 16.8 - - + +
185F GLU* 2.7 39.7 + - - +
186F TRP* 5.5 4.0 - - - -
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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