Contacts of the strand formed by residues 100 - 107 (chain K) in PDB entry 5M64
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 LEU 100 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64K GLN* 3.3 35.9 - - + +
65K ILE 3.3 16.8 - - - +
66K VAL* 3.6 20.2 - - + +
67K GLU 4.7 0.2 - - - +
68K GLU 5.7 0.2 - - - +
94K PRO* 3.2 28.1 - - + +
95K HIS 4.8 0.5 - - - +
98K GLU* 2.9 31.6 + - - +
99K ASN* 1.3 74.5 - - - +
101K LEU* 1.3 69.6 + - - +
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Residues in contact with LEU 101 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64K GLN* 2.9 13.4 - - - +
65K ILE* 2.8 43.1 + - + +
66K VAL 5.5 0.2 - - - -
68K GLU* 3.6 30.3 - - + +
69K ASP* 3.6 27.4 - - - +
70K HIS* 6.0 0.4 - - - +
73K GLY* 5.4 6.5 - - - -
91K TYR* 6.3 3.4 - - + -
92K SER 3.9 7.0 - - - +
93K ILE* 3.6 36.1 - - + -
94K PRO* 3.9 7.2 - - + -
95K HIS 5.5 0.7 - - - +
98K GLU 5.4 1.6 - - - +
100K LEU* 1.3 87.9 - - - +
102K ASN* 1.3 61.1 + - - +
103K ILE* 5.8 3.1 - - + -
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Residues in contact with ASN 102 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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697A TYR* 3.2 6.4 + - - +
701A ARG* 4.0 2.0 - - - +
703A GLU* 2.8 44.4 + - + +
50K LEU* 5.5 0.7 - - + -
62K SER* 6.2 2.7 - - - -
63K PHE 3.3 9.4 - - - +
64K GLN* 3.3 26.0 - - - +
65K ILE* 5.2 0.2 - - - -
92K SER* 2.4 65.0 + - - +
94K PRO* 3.4 18.0 - - - +
101K LEU* 1.3 75.1 - - - +
103K ILE* 1.3 63.5 + - - +
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Residues in contact with ILE 103 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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697A TYR* 3.8 1.1 - - - -
61K ALA 4.0 0.2 - - - +
62K SER* 3.8 1.6 - - - -
63K PHE* 2.9 64.9 + - + +
65K ILE* 5.2 15.0 - - + +
73K GLY* 5.1 9.4 - - - +
76K LEU* 4.6 23.6 - - + -
89K CYS* 6.0 0.9 - - - -
90K GLY 3.5 7.4 - - - +
91K TYR* 3.7 26.5 - - + -
101K LEU* 5.8 2.5 - - + -
102K ASN* 1.3 78.4 - - - +
104K ARG* 1.3 60.3 + - - +
105K ILE* 4.0 20.6 - - + -
117K LEU* 5.2 2.0 - - + -
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Residues in contact with ARG 104 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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697A TYR* 3.4 36.5 + - + +
702A PRO* 5.0 12.4 - - + +
710A SER 4.7 0.2 + - - -
711A LYS* 4.0 19.4 - - - +
53K ALA* 2.5 41.2 + - - +
54K THR* 3.4 8.7 - - - +
60K SER* 2.9 23.3 + - - -
61K ALA 3.3 12.4 - - - +
62K SER* 2.4 43.5 + - - +
88K PHE* 4.5 2.1 - - + -
89K CYS* 3.3 4.7 - - - -
90K GLY* 3.1 29.0 + - - -
103K ILE* 1.3 71.7 - - - +
105K ILE* 1.3 60.6 + - - +
106K GLN* 3.3 28.4 - - - +
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Residues in contact with ILE 105 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60K SER* 3.7 0.5 - - - -
61K ALA* 3.0 37.4 + - + +
63K PHE* 4.0 20.0 - - + -
76K LEU* 6.1 0.7 - - + -
80K ILE* 4.4 15.3 - - + -
86K VAL* 5.8 1.8 - - + -
88K PHE 3.6 4.7 - - - +
89K CYS* 3.6 27.8 - - + -
103K ILE* 4.0 16.8 - - + -
104K ARG* 1.3 73.5 - - - +
106K GLN* 1.3 68.1 + - - +
107K THR* 5.5 1.1 - - + +
113K ALA* 3.7 41.1 - - + +
116K ALA* 4.9 8.1 - - + -
117K LEU* 5.2 5.8 - - + +
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Residues in contact with GLN 106 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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702A PRO* 6.1 0.6 - - - +
711A LYS* 5.2 11.9 - - + +
712A ILE* 4.5 12.1 - - - +
59K THR* 3.7 5.2 - - + +
60K SER* 3.6 18.8 - - - -
86K VAL* 3.3 8.0 - - - +
87K GLU* 3.0 43.5 + - + +
88K PHE* 2.6 56.7 + - + +
104K ARG* 3.3 36.1 - - - +
105K ILE* 1.3 84.9 - - - +
107K THR* 1.3 61.1 + - - +
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Residues in contact with THR 107 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58K GLY 5.1 1.8 - - - +
59K THR* 3.3 39.9 + - - +
85K ASP* 2.4 43.6 + - - +
86K VAL* 4.6 1.6 - - - -
87K GLU* 3.4 12.6 - - - +
105K ILE* 5.7 1.8 - - + -
106K GLN* 1.3 75.5 - - - +
108K TYR* 1.3 58.4 + - - +
111K THR* 3.4 27.1 + - - +
112K THR 4.2 1.3 - - - -
113K ALA* 4.2 21.3 - - + +
116K ALA* 4.9 11.7 - - - +
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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