Contacts of the strand formed by residues 65 - 75 (chain k) in PDB entry 5Z58
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 MET 65 (chain k).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56k VAL* 6.0 4.3 - - + -
58k ALA 3.2 13.2 - - - +
59k PHE* 4.8 4.0 - - + -
63k CYS 4.3 5.2 - - - +
64k ASN* 1.3 76.5 - - - +
66k VAL* 1.3 63.4 + - - +
67k LEU* 4.0 5.3 + - + -
99k MET 3.8 0.3 - - - +
100k PHE* 3.2 5.4 - - - +
101k LEU* 2.7 45.1 + - + -
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Residues in contact with VAL 66 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76j LEU* 6.3 2.5 - - + -
56k VAL* 3.8 1.4 - - - -
57k LYS* 2.8 41.0 + - + +
58k ALA* 3.1 25.5 + - + +
65k MET* 1.3 72.6 - - - +
67k LEU* 1.3 55.6 + - - +
99k MET 3.3 7.6 - - - +
100k PHE* 4.5 3.6 - - + +
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Residues in contact with LEU 67 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54k GLY* 5.8 1.8 - - - -
55k ARG 3.3 11.4 - - - +
56k VAL* 5.0 0.7 - - - +
57k LYS* 5.3 2.0 - - - -
65k MET* 4.0 6.5 - - + +
66k VAL* 1.3 74.5 - - - +
68k GLU* 1.3 61.5 + - - +
70k VAL* 4.9 14.7 - - + +
96k ILE 5.2 0.3 - - - +
97k SER 3.5 4.2 - - - +
98k LYS* 3.6 2.1 - - - -
99k MET* 2.7 40.2 + - + +
101k LEU* 6.2 2.9 - - + -
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Residues in contact with GLU 68 (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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54k GLY* 3.7 1.6 - - - -
55k ARG* 3.0 40.7 + - + +
57k LYS* 5.1 7.8 - - + +
66k VAL 4.3 0.2 + - - -
67k LEU* 1.3 72.8 - - - +
69k ASN* 1.3 72.4 + - + +
70k VAL* 3.2 3.7 + - - +
97k SER 3.1 8.7 - - - +
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Residues in contact with ASN 69 (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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53k LEU 3.4 6.6 - - - +
54k GLY* 3.9 3.6 - - - -
55k ARG* 5.5 2.9 - - + +
68k GLU* 1.3 76.2 - - + +
70k VAL* 1.3 63.1 + - - +
71k LYS* 3.3 4.5 + - - +
96k ILE 4.0 2.9 - - - -
97k SER* 2.9 15.5 + - - +
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Residues in contact with VAL 70 (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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52k LEU* 5.3 8.5 - - + -
53k LEU 3.3 12.6 - - - +
54k GLY* 5.1 0.7 - - - -
67k LEU* 4.9 14.8 - - + +
68k GLU 4.0 5.6 - - - +
69k ASN* 1.3 72.6 - - - +
71k LYS* 1.3 62.7 + - - +
72k GLU* 3.8 2.4 + - + +
94k ARG 3.6 1.6 - - - +
95k TYR* 3.4 4.0 - - - +
96k ILE* 2.8 58.1 + - + +
99k MET* 5.8 4.5 - - + -
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Residues in contact with LYS 71 (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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51k LYS 3.7 1.6 - - - +
52k LEU* 4.6 0.4 - - - -
53k LEU* 2.7 48.5 + - + +
69k ASN 3.3 3.2 + - - +
70k VAL* 1.3 72.1 - - - +
72k GLU* 1.3 62.5 + - - +
73k MET* 3.8 2.4 + - + +
93k ASP* 6.0 3.4 - - + -
94k ARG 3.7 8.3 - - - +
95k TYR* 4.8 2.5 - - + +
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Residues in contact with GLU 72 (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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50k LYS* 5.8 4.7 - - + -
51k LYS 3.3 8.5 - - - +
52k LEU* 4.5 7.0 - - + +
70k VAL* 3.8 4.0 + - + +
71k LYS* 1.3 71.9 - - - +
73k MET* 1.3 58.7 + - - +
93k ASP* 3.1 7.3 - - - +
94k ARG* 2.9 42.3 + - + +
96k ILE* 6.0 4.5 - - + -
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Residues in contact with MET 73 (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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50k LYS* 3.6 1.1 - - - +
51k LYS* 2.8 44.2 + - + +
53k LEU* 6.5 0.4 - - + -
71k LYS 5.0 2.7 - - - +
72k GLU* 1.3 75.2 - - - +
74k TRP* 1.3 65.6 + - - +
92k LYS 3.5 9.2 - - - +
93k ASP* 4.6 5.6 - - + -
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Residues in contact with TRP 74 (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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49k ASN 4.1 9.9 - - - +
50k LYS* 4.1 17.9 - - + -
73k MET* 1.3 78.3 - - - +
75k THR* 1.3 68.5 + - - +
91k ASN* 3.6 4.7 - - - +
92k LYS* 2.9 35.0 + - + +
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Residues in contact with THR 75 (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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49k ASN 4.8 3.1 + - - +
74k TRP* 1.3 82.6 - - - +
76k GLU* 1.3 62.8 + - - +
89k PRO* 6.1 3.1 - - - -
90k VAL 3.4 11.2 - - - -
91k ASN* 4.6 5.2 - - - -
92k LYS* 4.7 1.3 - - - +
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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