Contacts of the strand formed by residues 60 - 69 (chain I) in PDB entry 4PHZ
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 GLU 60 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52I LYS* 3.1 25.6 + - - +
55I VAL* 3.7 1.9 - - - +
58I ASN 3.8 2.3 + - - +
59I GLU* 1.3 77.3 - - - +
61I MET* 1.3 76.8 + - - +
62I VAL* 5.3 3.1 - - + -
97I THR* 3.2 37.6 + - - +
123I ASN* 3.4 18.1 - - + +
124I LEU 3.3 14.5 - - - +
125I ARG* 3.7 21.5 + - - +
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Residues in contact with MET 61 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50I TRP* 3.7 32.5 - - + -
51I SER* 3.9 14.6 - - - +
52I LYS* 3.8 27.1 - - + +
55I VAL* 4.9 5.8 - - + -
60I GLU* 1.3 77.9 - - - +
62I VAL* 1.3 94.5 + - - +
63I LEU* 3.5 8.5 - - + +
94I LEU* 4.7 8.5 - - + -
123I ASN* 3.5 3.1 - - - -
124I LEU* 2.7 64.8 + - + +
134I VAL* 5.9 0.7 - - + -
153I ILE* 4.3 21.8 - - + -
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Residues in contact with VAL 62 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49I GLN 3.3 3.1 - - - +
51I SER* 2.7 48.5 + - - +
60I GLU* 5.3 4.0 - - + -
61I MET* 1.3 83.9 - - - +
63I LEU* 1.3 60.6 + - - +
64I SER* 4.4 18.2 - - - +
121I SER* 5.1 3.6 - - - -
122I ILE 3.2 8.3 - - - +
123I ASN* 3.1 24.9 - - + +
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Residues in contact with LEU 63 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48I VAL* 3.5 30.7 - - + -
49I GLN 3.4 5.2 - - - +
50I TRP* 3.3 26.2 - - + +
61I MET* 3.5 11.5 - - + +
62I VAL* 1.3 74.8 - - - +
64I SER* 1.3 70.9 + - - +
87I ALA* 5.6 0.2 - - - -
120I PHE* 4.7 1.6 - - + -
121I SER* 3.2 3.1 - - - -
122I ILE* 2.7 53.3 + - + +
124I LEU* 4.3 9.2 - - + -
134I VAL* 3.9 13.9 - - + -
135I HIS 3.6 30.1 - - - +
136I ALA* 4.2 10.1 - - + -
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Residues in contact with SER 64 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47I ASP 4.3 0.8 + - - -
48I VAL* 3.1 7.6 - - - +
49I GLN* 2.8 52.1 + - - +
62I VAL* 4.4 11.5 - - - +
63I LEU* 1.3 76.9 - - - +
65I GLY* 1.3 59.3 + - - +
120I PHE* 3.4 13.5 - - - -
121I SER* 3.6 17.3 - - - +
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Residues in contact with GLY 65 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46I TYR 3.8 2.2 - - - -
47I ASP 3.5 16.4 - - - -
48I VAL* 4.0 1.1 - - - -
64I SER* 1.3 77.5 - - - +
66I LYS* 1.3 67.0 + - - +
119I ALA* 3.3 4.2 - - - +
120I PHE* 2.8 46.2 + - - +
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Residues in contact with LYS 66 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45I TRP* 3.7 3.3 - - - +
46I TYR* 2.8 73.9 + - + +
47I ASP* 2.7 31.2 + - - +
48I VAL* 4.9 0.3 - - - +
49I GLN* 5.8 0.8 - - - +
65I GLY* 1.3 80.4 - - - +
67I VAL* 1.3 61.9 + - - +
118I TYR 3.2 8.7 - - - +
119I ALA* 4.3 6.5 - - + -
120I PHE* 3.9 6.5 - - - -
271I ILE* 3.8 19.7 - - + -
273I THR* 5.9 3.4 - - - -
276I THR* 6.0 0.2 - - - +
401I ARG* 4.7 3.1 - - - +
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Residues in contact with VAL 67 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43I LEU* 3.5 38.8 - - + -
44I ASN 3.3 11.7 - - - +
45I TRP* 3.8 23.8 - - + -
46I TYR* 4.0 4.0 - - - -
66I LYS* 1.3 76.8 - - - +
68I HIS* 1.3 63.7 + - - +
69I VAL* 4.1 1.0 + - + -
101I ILE* 4.7 2.2 - - + -
112I LEU* 5.1 3.4 - - + -
116I LYS 4.0 0.5 - - - +
117I ASP* 3.2 3.8 - - - +
118I TYR* 2.8 55.5 + - + +
120I PHE* 4.2 6.7 - - + -
138I ILE* 4.3 18.4 - - + -
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Residues in contact with HIS 68 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42I THR 3.5 0.9 - - - +
44I ASN* 2.7 42.9 + - + +
67I VAL* 1.3 74.7 - - - +
69I VAL* 1.3 58.8 + - - +
70I PHE* 3.0 17.7 + - - -
115I GLY* 3.2 25.1 + - - -
116I LYS 3.7 3.6 - - - -
117I ASP* 2.8 36.6 - - - +
277I VAL* 4.1 16.2 - - + +
391I LEU* 3.5 27.2 - - + +
405I GLU* 2.8 44.2 + - + -
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Residues in contact with VAL 69 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42I THR 3.8 4.0 - - - -
43I LEU* 4.1 13.7 - - + -
67I VAL* 5.1 2.0 - - + +
68I HIS* 1.3 68.9 + - - +
70I PHE* 1.3 58.6 - - - +
71I SER 3.4 0.2 + - - -
73I TRP* 3.9 16.8 - - + -
80I PRO* 4.2 7.2 - - + -
112I LEU* 3.9 22.0 - - + -
113I GLU 3.2 29.2 - - - +
114I ILE* 3.4 22.7 - - + -
115I GLY* 2.6 33.8 + - - -
116I LYS 3.0 14.2 + - - +
118I TYR* 4.0 10.3 - - + -
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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