Contacts of the helix formed by residues 99 - 115 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D ARG* 6.0 2.4 - - - +
43D PHE 3.1 27.1 - - - -
44D GLN* 3.9 7.6 - - - -
45D GLY 3.9 2.5 - - - +
97D ALA 3.7 0.6 + - - -
98D GLY* 1.3 74.5 - - - -
100D GLU* 1.3 62.2 + - - +
101D LEU 3.3 3.9 + - - -
102D SER* 3.4 5.2 + - - -
103D ASN* 3.1 39.0 + - - -
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Residues in contact with GLU 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D GLY* 3.2 16.3 - - - +
46D ALA* 4.2 4.4 - - + +
80D ALA* 3.6 5.2 - - + -
81D VAL 3.0 28.7 - - - +
82D PRO* 3.7 9.9 - - - +
83D ALA* 3.1 28.9 + - + +
94D GLU 4.3 6.0 - - - +
98D GLY* 3.2 26.5 - - - +
99D SER* 1.3 75.0 - - - +
101D LEU* 1.3 60.9 + - - +
103D ASN* 4.0 7.3 - - - +
104D ARG* 3.1 36.6 + - + +
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Residues in contact with LEU 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D PHE* 4.1 6.3 - - + -
45D GLY 3.0 17.7 + - - +
46D ALA 3.9 3.6 - - - +
47D GLY 3.7 25.6 - - - +
48D VAL 3.7 12.8 - - - +
49D TYR* 3.5 32.1 - - + -
80D ALA* 3.7 8.3 - - + +
100D GLU* 1.3 73.9 - - - +
102D SER* 1.3 60.4 + - - +
104D ARG* 3.3 3.1 + - - +
105D ILE* 3.0 43.1 + - + +
127D PHE* 4.2 8.5 - - + -
128D VAL 3.3 32.5 - - - +
129D ILE* 4.0 12.1 - - + -
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Residues in contact with SER 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D PRO* 5.7 1.5 - - - +
41D GLU 4.7 0.9 + - - -
42D ARG* 3.8 21.8 - - - +
43D PHE* 3.5 48.6 - - - -
99D SER* 3.4 7.1 + - - -
101D LEU* 1.3 78.4 - - - +
103D ASN* 1.3 59.9 + - - +
105D ILE* 3.1 6.7 + - - +
106D ARG* 2.9 41.6 + - - +
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Residues in contact with ASN 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D ARG* 4.3 20.4 - - - +
99D SER* 3.1 34.4 + - - +
100D GLU* 4.0 7.1 - - - +
102D SER* 1.3 79.7 + - - +
104D ARG* 1.3 58.7 + - + +
106D ARG* 3.2 10.9 + - - +
107D GLU* 2.9 33.2 + - - +
110D ARG* 4.8 2.1 + - - -
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Residues in contact with ARG 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D TYR* 4.3 13.5 - - + -
79D LYS 4.4 13.4 + - - +
80D ALA* 3.5 20.1 - - + +
81D VAL* 5.4 1.8 - - - +
100D GLU* 3.1 24.3 + - + +
101D LEU 3.8 3.4 - - - +
103D ASN* 1.3 76.5 - - + +
105D ILE* 1.3 59.0 - - - +
107D GLU* 3.6 29.2 + - - -
108D HIS* 2.5 41.8 + - + -
163D HIS* 4.0 21.3 - - - -
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Residues in contact with ILE 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D LEU* 3.5 24.5 - - + +
38D PRO* 4.4 0.2 - - + -
39D PRO* 3.5 31.0 - - + -
43D PHE* 4.5 6.3 - - + -
49D TYR* 3.6 42.6 - - + -
51D LEU* 5.5 0.2 - - + -
101D LEU* 3.0 26.5 + - + +
102D SER* 3.1 7.4 + - - +
104D ARG* 1.3 75.0 - - - +
106D ARG* 1.3 68.5 + - - +
108D HIS* 3.3 4.5 + - - +
109D GLY* 3.1 17.0 + - - -
125D CYS* 4.4 5.4 - - - -
127D PHE* 3.9 25.6 - - + -
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Residues in contact with ARG 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D PRO* 4.3 35.6 - - + +
39D PRO* 5.5 4.6 + - + -
41D GLU 6.2 0.2 - - - -
42D ARG* 3.6 52.2 - - - +
102D SER* 2.9 23.1 + - - +
103D ASN* 3.7 11.4 - - - +
105D ILE* 1.3 76.0 - - + +
107D GLU* 1.3 63.7 + - - +
109D GLY* 3.0 4.2 + - - -
110D ARG* 3.0 42.0 + - - +
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Residues in contact with GLU 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D ASN* 2.9 17.6 + - - +
104D ARG* 3.6 28.0 + - - +
105D ILE 3.1 0.2 - - - -
106D ARG* 1.3 78.5 - - - +
108D HIS* 1.3 71.4 + - + +
110D ARG* 3.3 38.9 + - - +
111D ASN* 3.4 21.9 + - - +
163D HIS* 2.8 36.3 + - + -
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Residues in contact with HIS 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D LEU* 5.1 0.9 - - + -
49D TYR* 3.0 25.8 + + + -
51D LEU* 4.6 9.6 - - + -
76D TYR* 4.4 6.7 - - - -
104D ARG* 2.5 40.0 + - - +
105D ILE* 4.0 4.0 - - - +
107D GLU* 1.3 92.2 + - + +
109D GLY* 1.3 65.1 + - - +
111D ASN* 3.1 20.8 + - - +
112D ILE* 3.2 12.7 + - - +
160D PHE* 3.2 43.0 + + + -
161D GLY* 4.3 25.6 - - - -
163D HIS* 5.1 3.9 + + - -
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Residues in contact with GLY 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D LEU* 4.1 16.3 - - - +
38D PRO* 5.4 2.2 - - - -
105D ILE 3.1 11.1 + - - -
106D ARG* 3.0 9.2 + - - -
108D HIS* 1.3 75.0 - - - +
110D ARG* 1.3 55.3 + - - +
112D ILE* 3.4 5.2 + - - +
113D ALA 2.9 21.5 + - - -
120D LEU* 3.5 29.6 - - - +
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Residues in contact with ARG 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D ASN 4.8 2.4 + - - -
106D ARG* 3.0 28.0 + - - +
107D GLU* 3.7 41.6 + - - +
108D HIS 3.2 0.6 - - - -
109D GLY* 1.3 72.6 - - - +
111D ASN* 1.3 61.4 + - - +
113D ALA* 3.0 12.8 + - + +
114D LYS* 2.9 44.9 + - - +
120D LEU* 5.5 0.2 - - - -
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Residues in contact with ASN 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D GLU* 3.4 17.8 + - - +
108D HIS* 3.1 17.2 + - - +
110D ARG* 1.3 75.8 + - - +
112D ILE* 1.3 65.9 + - - +
114D LYS* 3.1 36.5 + - - +
115D THR* 3.5 10.9 + - - +
160D PHE* 4.0 16.9 + - + -
162D ASN 4.4 4.6 + - - -
163D HIS* 6.1 2.4 - - - -
177D TRP* 4.2 5.0 - - + -
184D ARG* 3.2 40.2 + - - +
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Residues in contact with ILE 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D LEU* 3.6 30.3 - - + -
51D LEU* 4.9 2.0 - - + -
108D HIS 3.2 10.4 + - - +
109D GLY 3.5 6.1 - - - +
111D ASN* 1.3 76.4 - - - +
113D ALA* 1.3 62.3 + - - +
115D THR* 2.9 29.9 + - - -
118D LEU* 3.8 16.5 - - + +
120D LEU* 3.8 21.1 - - + +
123D PHE* 3.6 43.7 - - + -
153D TRP* 4.5 6.5 - - + -
160D PHE* 3.9 23.1 - - + -
177D TRP* 4.9 0.9 - - + -
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Residues in contact with ALA 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D GLY 2.9 14.8 + - - +
110D ARG* 3.0 19.0 + - + +
112D ILE* 1.3 76.1 - - - +
114D LYS* 1.3 58.9 + - - +
115D THR 3.4 6.4 + - - +
118D LEU 5.4 1.2 - - - +
120D LEU* 4.0 19.5 - - + +
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Residues in contact with LYS 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D ARG* 2.9 29.9 + - - +
111D ASN* 3.1 25.9 + - - +
113D ALA* 1.3 73.0 - - - +
115D THR* 1.3 68.0 + - + +
116D SER* 3.6 3.6 + - - -
183D GLY 4.0 26.5 + - - +
184D ARG* 4.7 17.5 - - + +
185D GLU 6.1 0.4 - - - +
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Residues in contact with THR 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D ASN 3.6 8.7 - - - +
112D ILE* 2.9 18.2 + - - +
113D ALA 3.5 7.3 - - - +
114D LYS* 1.3 82.2 - - + +
116D SER* 1.3 61.2 + - - +
117D ASN* 4.0 10.3 - - - -
118D LEU* 3.1 30.0 + - + +
177D TRP* 3.6 33.9 - - + -
181D HIS* 3.7 14.8 - - + +
182D PRO 3.3 13.0 - - - -
184D ARG 6.3 0.2 - - - +
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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
------------------------------------------------------------
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