Contacts of the helix formed by residues 118 - 127 (chain B) in PDB entry 1MBU
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 118 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27B VAL* 4.5 7.3 - - - +
28B GLU* 3.6 11.9 - - - -
83B SER* 4.5 6.7 - - - -
112B ILE 4.4 1.2 + - - -
115B GLU* 3.0 33.2 + - - +
116B GLN 3.4 1.8 - - - +
117B GLU* 1.3 80.6 - - - +
119B GLN* 1.3 63.6 + - - +
120B ALA* 3.6 2.6 + - - +
121B ALA* 3.0 18.2 + - - +
122B TYR* 3.3 18.0 + - - +
25D PRO* 4.2 2.9 - - - +
79D GLU* 4.4 12.3 - - - -
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Residues in contact with GLN 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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28B GLU* 3.2 7.4 + - + +
57B GLU 5.7 0.2 + - - -
61B PHE* 3.3 64.1 - - + +
117B GLU 4.0 0.8 + - - -
118B SER* 1.3 73.7 - - - +
120B ALA* 1.3 57.0 + - - +
122B TYR* 3.2 25.2 + - - +
123B LEU* 2.8 50.8 + - + +
24D PRO* 4.4 5.9 - - - +
25D PRO* 3.4 25.6 - - + +
79D GLU* 4.9 0.8 + - - -
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Residues in contact with ALA 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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27B VAL* 3.8 30.3 - - + +
28B GLU* 2.8 23.4 + - + +
31B LEU* 3.9 23.0 - - + +
58B LEU* 4.7 1.6 - - - -
112B ILE* 3.9 8.1 - - + -
118B SER* 3.1 0.4 - - - +
119B GLN* 1.3 77.6 - - - +
121B ALA* 1.3 63.6 + - - +
123B LEU* 3.3 4.3 + - - +
124B LEU* 2.9 26.5 + - - +
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Residues in contact with ALA 121 (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 ILE* 3.9 17.3 - - - +
113B PHE* 4.5 3.1 - - - +
115B GLU 3.4 25.4 - - - +
116B GLN* 4.7 3.4 - - - +
118B SER* 3.0 10.8 + - - +
120B ALA* 1.3 75.8 - - - +
122B TYR* 1.3 63.3 + - - +
124B LEU* 3.2 7.9 + - - +
125B ARG* 3.0 53.0 + - - +
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Residues in contact with TYR 122 (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 GLN 5.7 1.7 + - - +
118B SER 3.3 10.5 + - - +
119B GLN* 3.2 29.6 + - - +
121B ALA* 1.3 79.9 - - - +
123B LEU* 1.3 75.7 + - + +
125B ARG* 3.2 7.3 + - - +
126B LYS* 2.8 48.4 + - + +
22D LEU* 3.8 23.8 + - + -
23D LYS* 3.6 25.3 - - - +
24D PRO* 3.6 41.6 - - + +
25D PRO* 4.1 9.4 - - + -
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Residues in contact with LEU 123 (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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31B LEU* 5.4 0.2 - - + -
54B LEU* 3.8 14.4 - - + -
57B GLU* 3.8 38.6 - - + +
58B LEU* 3.7 34.5 - - + -
119B GLN* 2.8 42.8 + - + +
120B ALA* 3.9 3.6 - - - +
122B TYR* 1.3 83.0 - - + +
124B LEU* 1.3 66.9 + - - +
126B LYS* 3.5 19.5 - - - +
127B HIS* 3.0 31.5 + - - -
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Residues in contact with LEU 124 (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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31B LEU* 3.9 18.8 - - + -
44B LEU* 4.0 28.0 - - + -
54B LEU* 4.3 10.8 - - + -
109B LEU* 3.9 20.9 - - + -
112B ILE* 4.0 22.2 - - + -
113B PHE* 3.8 30.7 - - + -
120B ALA 2.9 21.5 + - - +
121B ALA* 3.6 5.4 - - - +
123B LEU* 1.3 76.9 - - - +
125B ARG* 1.3 60.8 + - - +
127B HIS* 3.2 8.3 + - - -
129B VAL* 3.0 35.6 + - + +
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Residues in contact with ARG 125 (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 PHE* 2.8 49.8 + - + +
116B GLN* 3.9 24.0 + - - +
121B ALA* 3.0 33.6 + - - +
122B TYR* 3.7 2.8 - - - +
124B LEU* 1.3 75.2 - - - +
126B LYS* 1.3 64.5 + - - +
128B GLU* 2.9 15.5 + - - +
129B VAL 3.7 15.3 - - - +
130B SER* 5.2 4.2 - - - +
131B ARG* 5.5 3.2 - - - +
22D LEU* 3.5 32.1 - - + +
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Residues in contact with LYS 126 (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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57B GLU* 3.0 36.0 + - - -
122B TYR* 2.8 43.8 + - + +
123B LEU* 3.1 21.0 + - - +
125B ARG* 1.3 75.5 - - - +
127B HIS* 1.3 69.6 + - - +
128B GLU* 3.3 10.7 + - - +
22D LEU* 3.8 8.0 - - + +
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Residues in contact with HIS 127 (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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47B CYS 5.1 3.5 - - - +
48B SER 5.7 0.3 - - - +
49B VAL* 4.4 27.0 - - + +
50B ASP* 4.3 14.5 + - + +
53B ALA* 4.1 18.6 - - + -
54B LEU* 3.7 23.0 - - + +
57B GLU* 2.6 40.1 + - - -
123B LEU 3.0 28.1 + - - +
124B LEU* 3.8 5.2 - - - +
125B ARG 3.1 0.2 - - - -
126B LYS* 1.3 84.6 + - + +
128B GLU* 1.3 73.0 + - - +
129B VAL* 3.3 9.1 + - + +
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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