Contacts of the strand formed by residues 59 - 67 (chain B) in PDB entry 1MPX
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 LYS 59 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51B MSE 3.8 39.6 - - + +
52B ILE 3.3 5.4 - - - +
53B PRO* 4.0 19.1 - - + -
57B GLY 3.9 12.8 - - - +
58B VAL* 1.3 73.0 - - - +
60B LEU* 1.3 64.0 + - - +
125B SER* 3.8 0.5 - - - -
126B GLU* 3.0 51.8 + - - +
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Residues in contact with LEU 60 (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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50B VAL 3.5 0.9 - - - +
51B MSE 4.3 2.2 - - - -
52B ILE* 2.9 29.6 + - - +
54B MSE 3.7 30.5 - - + -
58B VAL* 4.2 7.9 - - + -
59B LYS* 1.3 79.9 - - - +
61B HIS* 1.3 59.6 + - - +
62B THR* 3.1 10.4 + - - -
79B ARG* 3.4 29.6 - - - +
117B GLN* 3.5 24.0 - - - +
118B ASP 3.9 3.8 - - - +
120B ARG* 3.7 26.9 - - + +
125B SER* 3.2 15.3 - - - +
126B GLU 4.1 4.0 - - - +
149B ASP* 4.0 6.3 - - - +
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Residues in contact with HIS 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B GLU* 2.6 33.2 + - + +
50B VAL 4.4 4.0 - - - -
51B MSE 3.7 19.6 - - - -
60B LEU* 1.3 68.5 - - - +
62B THR* 1.3 64.3 + - - +
63B VAL* 3.8 12.7 - - + +
83B ASP* 5.7 0.7 - - - -
84B ALA* 4.6 0.3 - - - +
85B SER* 3.2 28.5 - - - -
116B PHE 4.4 0.3 - - - +
117B GLN* 3.5 0.7 - - - +
118B ASP* 2.8 51.2 + - - +
124B GLY* 3.4 33.3 - - - +
125B SER* 2.8 11.4 + - - +
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Residues in contact with THR 62 (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 ARG 3.9 0.3 - - - +
49B GLU* 3.4 4.3 - - - +
50B VAL* 2.9 51.2 + - + +
52B ILE* 3.5 16.6 - - + +
60B LEU 3.1 9.4 + - - -
61B HIS* 1.3 75.2 - - - +
63B VAL* 1.3 62.5 + - - +
64B ILE* 4.6 3.1 - - + -
115B VAL* 3.4 31.4 - - + -
116B PHE 3.6 6.1 - - - +
117B GLN* 3.0 31.6 + - + +
153B THR* 5.2 1.8 - - + -
157B LEU* 4.9 2.0 - - + -
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Residues in contact with VAL 63 (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 LYS* 3.8 30.7 - - + -
48B ARG 3.8 1.8 - - - -
49B GLU* 4.3 8.7 - - + +
61B HIS* 3.8 27.1 - - + +
62B THR* 1.3 75.0 - - - +
64B ILE* 1.3 63.6 + - - +
65B VAL* 4.2 2.5 - - + -
84B ALA* 3.9 15.9 - - + +
85B SER* 3.9 13.5 - - - +
88B THR* 3.6 28.0 - - + +
114B ARG 3.8 1.2 - - - +
115B VAL* 3.3 5.7 - - - +
116B PHE 2.8 34.3 + - - +
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Residues in contact with ILE 64 (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 ILE 3.5 3.5 - - - +
47B LYS* 3.5 0.7 - - - -
48B ARG* 2.8 53.2 + - + +
50B VAL* 4.0 33.7 - - + -
62B THR* 4.6 3.4 - - + -
63B VAL* 1.3 78.3 - - - +
65B VAL* 1.3 62.9 + - - +
66B LEU* 3.8 17.8 - - + +
113B ILE* 3.6 26.0 - - + -
114B ARG 3.6 2.5 - - - -
115B VAL* 4.0 19.1 - - + -
156B TRP* 4.4 2.0 - - + -
157B LEU* 4.1 16.4 - - + -
161B VAL* 4.1 17.9 - - + -
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Residues in contact with VAL 65 (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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45B TYR* 4.1 16.8 - - + -
46B ILE 3.6 2.9 - - - +
47B LYS* 3.9 26.7 - - + -
63B VAL* 4.5 2.2 - - + -
64B ILE* 1.3 75.0 - - - +
66B LEU* 1.3 62.1 + - - +
88B THR* 4.1 19.5 - - + -
96B MSE 3.7 35.3 - - + +
99B LEU* 4.1 11.2 - - + -
100B LEU* 4.1 10.8 - - + -
113B ILE* 3.5 3.4 - - - -
114B ARG* 2.8 40.5 + - + +
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Residues in contact with LEU 66 (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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45B TYR* 3.2 5.4 - - - -
46B ILE* 2.8 57.6 + - + +
48B ARG* 4.3 17.0 - - + +
64B ILE* 3.8 24.2 - - + +
65B VAL* 1.3 74.7 - - - +
67B PRO* 1.3 74.5 - - + +
70B ALA* 4.7 0.9 - - + -
96B MSE 4.5 0.9 - - - -
113B ILE* 3.9 17.5 - - + -
161B VAL* 4.1 8.1 - - + -
163B GLU* 3.5 47.1 - - + +
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Residues in contact with PRO 67 (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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44B ASP 3.9 9.0 - - - +
46B ILE* 5.7 0.2 - - - +
65B VAL 4.1 0.9 - - - +
66B LEU* 1.3 88.7 - - + +
68B LYS* 1.3 67.5 + - - +
69B GLY 3.4 0.3 + - - -
70B ALA* 3.1 30.5 + - + +
96B MSE 3.9 17.5 - - + -
108B VAL 5.7 1.3 - - - +
111B GLY* 4.0 21.8 - - - +
112B TYR 3.4 29.8 - - - +
113B ILE* 4.3 2.2 - - + -
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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