Contacts of the strand formed by residues 68 - 75 (chain P) in PDB entry 3E8E
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 HIS 68 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46P ILE* 3.7 22.7 - - + +
59P LEU* 3.8 15.6 - - + +
60P VAL 3.4 12.3 + - - +
61P LYS* 4.3 18.1 - - + +
66P GLY 3.8 11.6 + - - -
67P ASN* 1.3 74.8 - - - +
69P TYR* 1.3 72.2 + - - +
122P TYR* 4.2 17.2 + - + +
321P PRO* 3.9 20.3 + - + +
322P GLY* 3.6 35.2 - - - +
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Residues in contact with TYR 69 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43P PHE* 4.3 5.6 - + - -
59P LEU* 3.5 5.2 - - - +
60P VAL* 2.9 35.7 + - + +
62P HIS* 3.7 21.8 + + + -
65P THR* 4.9 0.3 + - - +
67P ASN* 3.0 46.9 + - + -
68P HIS* 1.3 79.1 - - - +
70P ALA* 1.3 60.9 + - - +
107P GLU* 3.6 34.9 - - + +
108P PHE* 4.3 19.2 - + - -
119P VAL* 3.5 24.2 - - + -
120P MET 3.4 16.6 - - - +
121P GLU* 4.7 2.9 - - - -
122P TYR* 3.8 10.5 - - - -
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Residues in contact with ALA 70 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49P LEU* 4.3 5.8 - - + -
57P VAL* 4.1 4.9 - - + -
58P MET 3.3 7.6 - - - +
69P TYR* 1.3 74.4 - - - +
71P MET* 1.3 59.5 + - - +
119P VAL* 3.4 3.6 - - - +
120P MET* 2.9 45.9 + - + +
121P GLU 3.9 1.3 - - - +
122P TYR* 3.9 3.5 - - - +
351P G98 3.6 43.7 - - + +
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Residues in contact with MET 71 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40P LEU* 4.1 12.6 - - + -
43P PHE* 3.7 34.1 - - + -
45P ARG* 4.7 3.6 - - - -
56P ARG 3.6 1.2 - - - +
57P VAL* 3.2 3.6 - - - -
58P MET* 2.8 36.1 + - + +
60P VAL* 3.7 26.2 - - + -
70P ALA* 1.3 74.3 - - - +
72P LYS* 1.3 66.0 + - - +
73P ILE* 3.7 22.0 + - + +
110P PHE* 4.0 10.5 - - + -
117P TYR* 3.8 20.6 - - + -
118P MET 3.4 6.7 - - - +
119P VAL* 3.5 24.7 - - + +
120P MET* 3.8 1.3 - - - -
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Residues in contact with LYS 72 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54P PHE* 5.4 0.7 - - - -
56P ARG 3.5 4.0 - - - +
57P VAL* 4.0 12.8 - - + -
71P MET* 1.3 72.8 - - - +
73P ILE* 1.3 62.1 + - - +
74P LEU* 3.5 25.5 - - + +
91P GLU* 3.1 28.3 + - - +
116P LEU 3.6 1.2 - - - +
117P TYR* 3.4 6.6 - - - -
118P MET* 2.8 44.7 + - + +
120P MET* 3.3 15.4 - - + +
184P ASP* 3.0 28.1 + - - -
186P GLY* 5.0 0.6 - - - -
351P G98 3.1 58.9 + - + -
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Residues in contact with ILE 73 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45P ARG* 4.6 2.2 - - - -
55P GLY* 3.1 5.2 - - - -
56P ARG* 2.8 40.0 + - + +
58P MET* 3.8 28.0 - - + -
71P MET* 3.8 26.2 - - + +
72P LYS* 1.3 75.2 - - - +
74P LEU* 1.3 62.8 - - - +
75P ASP 4.1 0.2 + - - -
115P ASN* 3.8 22.0 - - + +
116P LEU 3.4 2.0 - - - -
117P TYR* 3.5 27.1 - - + -
335P ILE* 3.6 34.1 - - + -
351P G98 4.8 0.5 - - - -
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Residues in contact with LEU 74 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54P PHE* 3.5 24.5 - - + +
72P LYS* 3.5 35.2 - - + +
73P ILE* 1.3 74.7 - - - +
75P ASP* 1.3 62.1 + - - +
76P LYS 3.2 0.7 + - - -
79P VAL* 4.0 11.4 - - + -
88P THR* 3.6 31.9 - - + -
91P GLU* 4.6 5.8 - - - +
115P ASN* 3.1 8.7 - - - -
116P LEU* 2.8 57.3 + - + +
118P MET* 3.6 24.7 - - + -
351P G98 5.1 1.6 - - + -
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Residues in contact with ASP 75 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54P PHE 2.8 17.3 + - - +
55P GLY* 4.5 1.5 - - - -
73P ILE* 4.1 1.6 + - - +
74P LEU* 1.3 67.8 - - - +
76P LYS* 1.3 66.0 + - - +
77P GLN* 2.9 25.6 + - - +
78P LYS* 3.0 47.1 + - + +
79P VAL* 3.0 13.3 + - - +
114P SER* 4.1 4.3 - - - +
115P ASN* 3.5 15.9 + - - +
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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
------------------------------------------------------------
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