Contacts of the strand formed by residues 115 - 120 (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 ASN 115 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73P ILE* 3.8 15.6 - - + +
74P LEU 3.1 7.4 - - - +
75P ASP* 3.5 19.6 + - - +
76P LYS* 4.1 4.7 - - - -
111P LYS* 3.3 6.2 - - - +
112P ASP* 2.8 36.6 + - - +
114P SER* 1.3 93.6 - - - +
116P LEU* 1.3 61.8 + - - +
117P TYR* 2.9 35.1 + - + +
335P ILE* 3.7 19.6 - - - +
336P ARG 4.2 7.1 + - - +
337P VAL* 4.5 1.0 - - - +
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Residues in contact with LEU 116 (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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72P LYS 3.6 0.5 - - - +
73P ILE* 3.4 5.0 - - - -
74P LEU* 2.8 51.9 + - + +
76P LYS* 3.8 28.3 - - + -
79P VAL* 4.8 1.8 - - + -
88P THR* 3.8 21.8 - - + +
110P PHE 3.9 2.5 - - - -
111P LYS* 4.0 9.0 - - + -
115P ASN* 1.3 74.8 - - - +
117P TYR* 1.3 62.4 + - - +
347P PHE* 3.6 37.2 - - + -
350P PHE* 3.8 40.6 - - + -
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Residues in contact with TYR 117 (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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40P LEU* 3.5 30.3 - - + +
71P MET* 3.8 22.2 - - + -
72P LYS 3.4 4.3 - - - +
73P ILE* 3.5 28.9 - - + -
109P SER* 3.3 5.9 - - - -
110P PHE* 2.8 78.7 + + + +
111P LYS* 4.1 0.9 - - - -
112P ASP* 2.6 39.2 + - + -
115P ASN* 2.9 32.7 + - + -
116P LEU* 1.3 73.8 - - - +
118P MET* 1.3 65.9 + - - +
119P VAL 4.3 0.2 - - - -
335P ILE* 4.0 3.0 - - + +
337P VAL* 3.9 1.7 - - - +
350P PHE* 3.8 1.7 - - - -
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Residues in contact with MET 118 (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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71P MET* 3.4 1.1 - - - +
72P LYS* 2.8 48.2 + - + -
74P LEU* 3.6 31.6 - - + -
88P THR* 4.8 1.8 - - - +
91P GLU* 3.6 43.3 - - + +
92P LYS* 4.2 18.2 - - + -
95P LEU* 4.5 3.4 - - - -
106P LEU* 3.7 15.7 - - + -
108P PHE 3.7 4.0 - - - -
109P SER* 4.6 4.3 - - - -
117P TYR* 1.3 77.7 - - - +
119P VAL* 1.3 62.0 + - - +
120P MET* 3.2 5.4 - - - +
350P PHE* 3.9 20.2 - - + -
351P G98 4.1 11.9 - - + -
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Residues in contact with VAL 119 (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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43P PHE* 4.1 11.4 - - + -
60P VAL* 4.8 1.6 - - + -
69P TYR* 3.5 35.2 - - + -
70P ALA 3.4 5.2 - - - +
71P MET* 3.5 32.3 - - + -
106P LEU* 3.5 2.5 - - - +
107P GLU* 2.7 30.4 + - - -
108P PHE* 2.9 38.7 + - + +
110P PHE* 4.0 19.5 - - + -
118P MET* 1.3 74.5 - - - +
120P MET* 1.3 57.8 + - - +
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Residues in contact with MET 120 (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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57P VAL* 4.7 4.0 - - + -
69P TYR* 3.4 6.8 - - - +
70P ALA* 2.9 44.5 + - + +
71P MET 3.8 0.7 - - - -
72P LYS* 3.3 23.3 - - + +
104P VAL* 5.1 1.8 - - + -
105P LYS 3.2 19.7 - - - +
106P LEU* 4.2 6.7 - - + -
107P GLU* 4.0 8.7 - - - -
118P MET 3.2 28.5 - - - +
119P VAL* 1.3 75.8 - - - +
121P GLU* 1.3 76.2 + - - +
122P TYR 3.4 0.3 + - - -
351P G98 3.6 56.5 - - + +
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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