Contacts of the strand formed by residues 90 - 101 (chain h) in PDB entry 5MQF
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 VAL 90 (chain h).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75h THR* 3.4 4.2 - - - -
76h GLU* 2.8 48.8 + - + +
77h VAL 3.9 11.0 - - - +
78h PRO* 5.5 2.0 - - + -
88h LYS 4.4 1.3 - - - +
89h PRO* 1.3 76.3 - - - +
91h ASN* 1.3 66.1 + - - +
92h LYS* 4.9 0.4 - - + +
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Residues in contact with ASN 91 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74h TRP 3.6 8.5 - - - +
75h THR* 4.3 5.2 - - - +
90h VAL* 1.3 78.9 - - - +
92h LYS* 1.3 61.9 + - - +
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Residues in contact with LYS 92 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73h MET* 3.5 3.1 - - - +
74h TRP* 2.9 39.5 + - + +
75h THR* 5.3 0.9 - - - +
76h GLU* 5.6 6.5 - - + -
90h VAL* 4.9 2.5 - - + +
91h ASN* 1.3 76.7 - - - +
93h ASP* 1.3 65.4 + - - +
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Residues in contact with ASP 93 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71h LYS* 5.9 4.3 - - + -
72h GLU 3.1 14.6 - - - +
73h MET* 4.3 6.7 - - + -
92h LYS* 1.3 77.7 - - - +
94h ARG* 1.3 66.8 + - - +
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Residues in contact with ARG 94 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70h VAL 3.6 1.2 - - - +
71h LYS* 3.7 2.8 - - - -
72h GLU* 3.0 39.3 + - + +
93h ASP* 1.3 78.8 - - - +
95h TYR* 1.3 63.6 + - - +
96h ILE* 5.1 0.7 - - - +
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Residues in contact with TYR 95 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69h ASN 6.4 0.2 - - - -
70h VAL 3.4 6.3 - - - +
71h LYS* 4.8 2.5 - - + +
94h ARG* 1.3 75.3 - - - +
96h ILE* 1.3 60.0 + - - +
97h SER 4.2 0.9 - - - +
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Residues in contact with ILE 96 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69h ASN 4.8 0.4 - - - -
70h VAL* 2.7 49.0 + - + +
72h GLU* 6.0 4.3 - - + +
94h ARG 5.1 1.3 - - - +
95h TYR* 1.3 74.1 - - - +
97h SER* 1.3 65.9 + - - +
98h LYS* 3.4 4.7 + - - +
99h MET* 5.1 11.0 - - + -
69n ILE* 5.9 5.6 - - + -
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Residues in contact with SER 97 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67h LEU 4.2 0.4 - - - -
68h GLU* 3.1 12.5 - - - +
69h ASN* 3.0 29.5 + - - +
95h TYR* 4.2 0.6 - - - +
96h ILE* 1.3 72.1 - - - +
98h LYS* 1.3 63.0 + - - +
72n ASP* 4.9 17.0 - - - -
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Residues in contact with LYS 98 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67h LEU 3.6 4.3 - - - +
68h GLU* 6.3 0.2 - - + -
96h ILE* 3.4 2.6 - - - +
97h SER* 1.3 84.3 + - - +
99h MET* 1.3 59.2 + - - +
69n ILE* 3.8 3.3 - - - +
70n LEU* 2.8 39.7 + - + +
71n PRO 4.0 21.3 - - - +
72n ASP* 4.8 5.8 - - - +
74n LEU* 5.5 4.7 - - + +
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Residues in contact with MET 99 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65h MET 3.8 0.3 - - - +
66h VAL* 3.3 4.5 - - - +
67h LEU* 2.7 45.8 + - + +
70h VAL* 5.8 3.6 - - + -
96h ILE* 5.1 11.9 - - + +
98h LYS* 1.3 74.5 - - - +
100h PHE* 1.3 61.0 + - - +
101h LEU 4.2 0.2 - - - -
67n TYR* 5.7 2.9 - - + -
68n PHE 3.1 14.6 - - - +
69n ILE* 4.1 7.2 - - + -
70n LEU* 4.1 7.0 - - - +
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Residues in contact with PHE 100 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65h MET 3.2 8.5 - - - +
66h VAL* 4.5 3.4 - - + +
99h MET* 1.3 73.9 - - - +
101h LEU* 1.3 59.9 - - - +
102h ARG 4.1 0.4 + - - -
7n LEU* 6.6 0.4 - - + -
67n TYR* 2.9 7.2 - - - +
68n PHE* 2.6 53.9 + - + -
70n LEU* 5.2 1.7 - - + +
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Residues in contact with LEU 101 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63h CYS 3.9 2.4 - - - +
64h ASN* 3.0 9.1 - - - +
65h MET* 2.7 43.8 + - + +
67h LEU* 6.2 3.1 - - + -
99h MET 4.3 0.4 + - - -
100h PHE* 1.3 72.4 - - - +
102h ARG* 1.3 61.1 + - - +
66n ARG 4.8 0.4 - - - +
67n TYR* 3.7 11.0 - - + -
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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