Contacts of the strand formed by residues 75 - 85 (chain B) in PDB entry 4MVL
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 75 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B PHE* 3.4 10.9 - - - -
72B ASP 3.0 32.2 + - - +
73B ASP* 3.4 17.7 - - + +
74B LYS* 1.3 83.5 - - + +
76B CYS* 1.3 62.2 + - - +
77B LEU* 3.8 22.3 + - + +
175B CYS* 4.2 0.4 - - - -
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Residues in contact with CYS 76 (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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70B GLY 3.6 0.2 - - - -
75B LYS* 1.3 74.8 - - - +
77B LEU* 1.3 65.9 + - - +
78B TYR* 3.6 34.6 - - + +
175B CYS* 2.0 54.1 - - + -
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Residues in contact with LEU 77 (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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68B SER 3.4 1.4 - - - +
69B VAL* 3.5 3.3 - - - +
70B GLY 2.7 41.4 + - - +
72B ASP* 3.6 33.9 - - + +
75B LYS* 4.1 28.7 - - + +
76B CYS* 1.3 79.2 - - - +
78B TYR* 1.3 64.1 + - - +
18F VAL* 3.6 19.5 - - + -
19F PHE* 3.3 17.0 - - + -
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Residues in contact with TYR 78 (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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67B THR* 4.4 17.5 - - + -
68B SER 3.3 5.4 - - - +
69B VAL* 3.6 30.2 - - + +
76B CYS* 3.6 42.4 - - + +
77B LEU* 1.3 79.0 - - - +
79B LYS* 1.3 60.5 - - - +
80B ILE* 4.0 15.4 + - + +
175B CYS* 4.8 2.6 + - - -
19F PHE* 4.4 2.5 - - - -
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Residues in contact with LYS 79 (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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66B VAL 3.1 1.7 - - - +
67B THR* 3.1 1.8 - - - +
68B SER* 2.9 23.8 + - - -
78B TYR* 1.3 72.7 - - - +
80B ILE* 1.3 62.0 + - - +
81B ARG* 2.8 48.0 + - - +
19F PHE* 3.7 54.2 + - + +
21F ALA 4.6 2.8 + - - -
22F GLU* 5.3 0.2 + - - -
23F ASP* 3.0 25.4 + - - -
25F GLY* 4.1 10.3 - - - +
26F SER* 3.1 33.3 + - - +
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Residues in contact with ILE 80 (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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65B ASN* 4.0 23.3 - - - +
66B VAL 3.4 2.5 - - - +
67B THR* 3.8 26.9 - - + +
78B TYR* 4.0 16.7 + - + +
79B LYS* 1.3 80.0 - - - +
81B ARG* 1.3 65.7 + - - +
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Residues in contact with ARG 81 (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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65B ASN* 4.5 2.7 - - - -
66B VAL* 2.7 65.5 + - - +
68B SER* 2.9 22.0 + - - +
79B LYS* 2.8 51.4 + - - +
80B ILE* 1.3 80.0 - - - +
82B THR* 1.3 59.1 + - - +
83B PHE* 3.9 10.8 - - + -
94B LEU* 5.0 4.7 - - + -
22F GLU* 2.9 31.9 + - - +
23F ASP* 3.0 40.6 + - - +
26F SER* 4.4 12.8 - - - +
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Residues in contact with THR 82 (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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59B LYS* 6.3 0.7 - - + -
63B SER* 4.2 18.4 - - - +
64B TYR 3.4 12.1 - - - +
65B ASN* 4.0 11.3 + - - +
81B ARG* 1.3 76.0 - - - +
83B PHE* 1.3 72.3 + - - +
84B VAL* 3.9 12.5 + - + +
93B THR 4.0 0.2 - - - +
94B LEU* 3.9 19.2 - - - +
95B GLY 5.0 1.0 + - - -
96B ARG* 6.2 4.7 - - - -
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Residues in contact with PHE 83 (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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56B TYR* 4.0 23.3 - + - -
63B SER* 3.2 8.9 - - - -
64B TYR* 2.8 41.3 + - + +
66B VAL* 3.6 25.8 - - + -
81B ARG* 3.9 11.2 - - + -
82B THR* 1.3 77.4 - - - +
84B VAL* 1.3 61.6 + - - +
85B PRO 3.9 0.2 - - - -
92B PHE* 4.0 20.3 - + + -
93B THR 3.5 6.3 - - - -
94B LEU* 4.8 6.5 - - + -
108B VAL* 3.6 32.3 - - + -
123B PHE* 3.7 21.8 - + - -
22F GLU* 6.3 0.2 - - - -
23F ASP* 3.2 33.7 - - + -
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Residues in contact with VAL 84 (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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63B SER* 4.6 3.8 - - - -
82B THR* 3.9 15.3 + - + +
83B PHE* 1.3 72.4 - - - +
85B PRO* 1.4 83.1 - - + +
92B PHE* 3.3 2.7 - - - -
93B THR* 2.6 53.5 + - + +
95B GLY* 4.9 14.8 - - - +
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Residues in contact with PRO 85 (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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61B ASP 3.9 5.6 - - - +
62B LYS* 3.3 40.4 - - + +
63B SER* 3.8 16.4 - - - -
83B PHE 3.9 0.2 - - - -
84B VAL* 1.4 108.8 - - + +
86B GLY* 1.3 62.9 + - - +
91B GLU 3.5 7.2 - - - +
92B PHE* 3.9 7.0 - - + -
93B THR* 4.1 4.3 - - - +
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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