Contacts of the helix formed by residues 102 - 119 (chain B) in PDB entry 1MUC
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 THR 102 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B GLU* 3.1 2.8 + - - -
100B GLY* 4.2 14.8 - - - +
101B ASN* 1.3 74.3 - - - +
103B PHE* 1.3 68.0 + - - +
105B LYS* 4.2 6.5 - - + +
106B SER* 2.8 31.9 + - - -
253B GLU 4.2 11.0 + - - +
254B SER* 5.3 4.3 - - - -
275B ALA 2.8 21.2 + - - -
276B LYS* 3.8 19.8 + - - +
277B ASN 3.9 13.7 - - - +
278B GLY* 3.5 14.9 - - - -
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Residues in contact with PHE 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ALA* 3.3 14.4 - - + +
52B THR 3.2 33.4 - - - -
53B THR* 3.6 23.3 - - - -
59B TYR 5.1 3.8 - - - -
60B GLY* 5.4 8.7 - - - -
61B TYR 5.7 0.9 - - - -
62B GLU* 3.0 34.9 + - + +
67B ILE* 4.0 14.1 - - + -
102B THR* 1.3 77.3 - - - +
104B ALA* 1.3 66.7 + - - +
106B SER* 3.3 5.6 + - - -
107B GLY 3.0 18.7 + - - -
275B ALA* 3.3 30.7 - - + +
276B LYS* 3.9 29.4 - - + -
302B MET* 4.0 13.9 - - + -
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Residues in contact with ALA 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ALA* 4.4 2.6 - - - +
62B GLU* 3.2 14.0 + - - +
67B ILE* 4.3 19.2 - - + +
70B ASN* 5.7 0.9 - - + -
71B ILE* 4.1 15.5 - - + +
75B LEU* 3.6 25.8 - - + -
101B ASN* 3.8 7.6 - - + +
103B PHE* 1.3 78.1 - - - +
105B LYS* 1.3 62.4 + - - +
107B GLY* 3.2 2.6 + - - -
108B ILE* 3.1 28.9 + - - +
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Residues in contact with LYS 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B LEU* 5.2 5.6 - - + -
91B MET* 3.5 22.8 - - + +
94B LEU* 3.8 24.2 - - + -
95B ASP* 2.9 28.2 + - - +
98B ALA* 2.8 31.1 + - - -
100B GLY* 2.8 31.7 + - - +
101B ASN* 3.0 16.3 + - + +
102B THR* 3.7 11.1 - - + +
104B ALA* 1.3 77.8 - - - +
106B SER* 1.3 55.9 + - - +
108B ILE* 3.3 5.8 + - - -
109B GLU* 2.8 31.4 + - - +
278B GLY* 3.7 11.2 - - - +
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Residues in contact with SER 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B GLU 4.6 4.0 + - - -
51B ALA* 5.9 0.4 - - - -
102B THR 2.8 22.2 + - - -
103B PHE 3.4 5.4 - - - -
105B LYS* 1.3 73.1 - - - +
107B GLY* 1.3 54.9 + - - +
109B GLU* 4.0 0.9 - - - +
110B SER* 2.6 38.7 + - - -
274B ILE* 3.4 37.3 + - - +
275B ALA* 3.8 7.9 + - - +
278B GLY 3.6 0.4 + - - -
279B GLY* 3.5 25.3 - - - -
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Residues in contact with GLY 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU* 3.9 15.8 - - - +
49B GLY* 3.6 11.3 - - - -
50B GLU 3.5 28.2 + - - -
51B ALA* 4.4 0.4 - - - -
103B PHE 3.0 12.5 + - - -
104B ALA 3.2 3.3 + - - -
106B SER* 1.3 77.3 + - - +
108B ILE* 1.3 61.7 + - - +
110B SER 3.5 0.2 + - - -
111B ALA* 3.2 19.1 + - - +
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Residues in contact with ILE 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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9B ILE* 5.1 10.1 - - + -
37B LEU* 4.4 17.7 - - + -
39B VAL* 4.9 3.5 - - + +
71B ILE* 4.4 12.1 - - + -
75B LEU* 4.0 32.1 - - + -
76B ALA 5.2 0.4 - - - +
79B LEU* 3.6 29.2 - - + -
91B MET* 4.4 1.6 - - - -
94B LEU* 4.2 17.9 - - + -
104B ALA 3.1 17.0 + - - +
105B LYS* 3.7 4.9 - - - +
107B GLY* 1.3 75.6 - - - +
109B GLU* 1.3 64.8 + - - +
111B ALA* 3.3 5.9 + - - +
112B LEU* 3.1 35.0 + - + +
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Residues in contact with GLU 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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87B ILE* 4.2 9.4 - - + -
91B MET* 3.6 20.3 - - + +
105B LYS 2.8 20.3 + - - +
106B SER 4.0 2.9 - - - +
108B ILE* 1.3 72.7 - - - +
110B SER* 1.3 58.5 + - - +
112B LEU* 3.2 4.6 + - - +
113B LEU* 2.9 38.6 + - + +
278B GLY 4.2 6.2 - - - +
279B GLY* 3.1 6.2 - - - -
280B PRO* 3.0 14.4 - - + +
281B ARG* 2.8 70.1 + - - +
282B ALA 3.8 1.5 + - - -
285B ARG* 4.6 2.4 + - - -
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Residues in contact with SER 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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48B ILE 3.7 3.3 - - - +
49B GLY* 4.1 11.2 - - - -
50B GLU 4.6 4.1 + - - -
106B SER* 2.6 26.4 + - - -
107B GLY* 3.7 6.0 - - - -
109B GLU* 1.3 78.3 - - - +
111B ALA* 1.3 55.6 + - - +
113B LEU* 3.4 4.8 + - - +
114B ASP* 2.9 28.4 + - - +
274B ILE* 4.2 2.8 - - - +
280B PRO* 3.5 23.4 - - - +
307B ILE* 5.7 0.4 - - - -
308B GLY* 6.4 0.2 - - - -
311B ALA* 3.7 21.5 - - - +
358B LEU* 4.1 6.4 - - - +
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Residues in contact with ALA 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU* 4.4 4.3 - - + -
39B VAL* 3.5 29.4 - - + -
47B GLY* 3.3 15.1 - - - +
48B ILE 3.4 27.1 + - - -
49B GLY* 3.7 4.0 - - - +
107B GLY 3.2 11.5 + - - +
108B ILE 3.7 2.5 - - - +
109B GLU 3.2 0.2 - - - -
110B SER* 1.3 77.5 - - - +
112B LEU* 1.3 59.5 + - - +
114B ASP 3.3 0.3 + - - -
115B ALA* 2.9 25.5 + - - +
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Residues in contact with LEU 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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6B ILE* 3.9 26.0 - - + -
39B VAL* 4.1 22.9 - - + -
41B CYS* 5.6 1.3 - - - -
79B LEU* 4.9 2.5 - - + -
84B ALA* 4.5 15.4 - - + +
87B ILE* 3.7 25.1 - - + +
90B ALA* 4.0 27.1 - - + -
91B MET* 4.3 10.8 - - - -
108B ILE* 3.1 34.9 + - + +
109B GLU 3.7 4.0 - - - +
111B ALA* 1.3 76.5 - - - +
113B LEU* 1.3 57.8 + - - +
115B ALA* 3.5 5.1 + - + +
116B GLN* 2.9 30.5 + - - +
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Residues in contact with LEU 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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87B ILE* 3.6 21.5 - - + -
109B GLU* 2.9 31.8 + - + +
110B SER* 3.7 4.3 - - - +
112B LEU* 1.3 73.9 - - - +
114B ASP* 1.3 61.0 + - - +
116B GLN* 4.4 0.7 - - - -
117B GLY 2.9 24.1 + - - -
124B VAL* 3.4 25.3 - - + +
127B LEU* 3.4 24.8 - - + +
128B LEU* 4.3 16.8 - - + -
280B PRO* 3.7 35.9 - - + -
281B ARG* 4.2 15.0 - - + -
358B LEU* 5.8 0.4 - - + -
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Residues in contact with ASP 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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46B GLU 4.1 0.2 - - - +
47B GLY* 3.4 4.2 - - - -
48B ILE* 2.9 38.2 + - - +
110B SER 2.9 17.8 + - - +
111B ALA 3.5 5.6 - - - +
113B LEU* 1.3 77.9 - - - +
115B ALA* 1.3 61.6 + - - +
117B GLY 3.3 0.2 + - - -
118B LYS* 3.0 42.6 + - - +
124B VAL* 4.1 8.0 - - - +
357B GLY* 3.5 4.0 - - - -
358B LEU* 2.8 40.4 + - + +
359B GLY 4.4 0.9 + - - -
360B LEU 5.1 1.3 - - - +
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Residues in contact with ALA 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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39B VAL* 5.1 1.6 - - + +
41B CYS* 4.2 13.9 - - - -
45B VAL* 3.4 21.0 - - + +
46B GLU 4.2 0.9 - - - -
47B GLY* 3.7 19.0 - - - +
111B ALA 2.9 17.4 + - - +
112B LEU* 3.7 7.4 - - + +
114B ASP* 1.3 76.8 - - - +
116B GLN* 1.3 57.0 + - - +
118B LYS 3.3 1.0 + - - -
119B ARG* 2.9 41.8 + - - +
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Residues in contact with GLN 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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84B ALA 5.0 0.4 - - - +
85B ASP* 3.4 32.3 + - - +
87B ILE* 4.1 14.6 - - + -
112B LEU 2.9 19.3 + - - +
113B LEU 3.9 3.1 - - - +
114B ASP 3.3 0.2 - - - -
115B ALA* 1.3 76.7 - - - +
117B GLY* 1.3 57.2 + - - +
119B ARG* 3.0 35.3 + - - +
120B LEU* 3.0 54.5 + - - +
127B LEU* 4.0 20.4 - - + +
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Residues in contact with GLY 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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113B LEU 2.9 14.1 + - - -
114B ASP 3.8 1.6 - - - -
116B GLN* 1.3 78.2 - - - +
118B LYS* 1.3 56.4 + - - +
120B LEU 4.6 0.2 - - - -
121B GLY* 2.8 8.8 + - - -
122B LEU 2.8 47.1 + - - +
127B LEU* 3.4 15.8 - - - +
356B PRO* 3.7 1.2 - - - +
357B GLY* 3.6 6.7 - - - -
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Residues in contact with LYS 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B VAL* 3.8 13.6 - - + +
46B GLU* 3.5 28.0 + - - +
48B ILE* 5.8 3.2 - - - +
114B ASP* 3.0 39.7 + - - +
115B ALA 3.6 6.1 - - - +
117B GLY* 1.3 76.8 - - - +
119B ARG* 1.3 61.9 + - - +
121B GLY* 3.5 8.7 + - - -
356B PRO* 4.0 17.5 - - + +
357B GLY* 3.8 6.2 - - - +
360B LEU 4.2 17.9 + - - +
361B THR* 5.0 9.8 - - - +
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Residues in contact with ARG 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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4B ALA* 3.7 11.1 - - - +
41B CYS* 3.8 11.9 - - - +
43B ASP* 3.0 41.3 + - - +
45B VAL* 4.1 15.4 - - + +
84B ALA* 3.6 29.7 + - - +
85B ASP* 4.6 6.4 - - - +
112B LEU 4.9 0.2 + - - -
115B ALA* 2.9 22.0 + - - +
116B GLN* 3.0 42.4 + - - +
117B GLY 3.2 0.2 - - - -
118B LYS* 1.3 79.8 - - - +
120B LEU* 1.3 69.7 + - + +
121B GLY 3.4 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
------------------------------------------------------------
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