Contacts of the strand formed by residues 115 - 121 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73I ILE* 3.8 15.3 - - + +
74I LEU 3.4 4.3 - - - +
75I ASP* 3.7 21.1 + - - +
76I LYS* 3.7 2.0 - - - +
111I LYS* 3.2 7.3 - - - +
112I ASP* 2.7 35.7 + - - +
114I SER* 1.3 86.5 - - - +
116I LEU* 1.3 63.3 + - - +
117I TYR* 3.0 35.0 + - + +
335I ILE* 4.0 14.3 - - - +
336I ARG 3.7 19.9 + - - +
337I VAL* 4.5 1.4 - - - +
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Residues in contact with LEU 116 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72I LYS 3.6 0.6 - - - +
73I ILE* 3.4 5.5 - - - -
74I LEU* 2.9 49.1 + - + +
76I LYS* 3.8 24.2 - - + -
79I VAL* 5.0 1.8 - - + -
88I THR* 4.1 16.6 - - + -
110I PHE 3.9 2.9 - - - -
111I LYS* 3.9 19.3 - - + -
115I ASN* 1.3 74.1 - - - +
117I TYR* 1.3 64.2 + - - +
347I PHE* 3.6 37.7 - - + -
350I PHE* 3.9 38.1 - - + -
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Residues in contact with TYR 117 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40I LEU* 3.7 29.3 - - + +
71I MET* 3.8 22.7 - - + -
72I LYS 3.4 2.7 - - - +
73I ILE* 3.6 26.0 - - + -
109I SER* 3.2 8.5 - - - -
110I PHE* 2.7 78.2 + + + +
112I ASP* 2.7 35.8 + - - -
115I ASN* 3.0 36.8 + - + -
116I LEU* 1.3 76.5 - - - +
118I MET* 1.3 66.3 + - - +
335I ILE* 4.1 2.8 - - + +
337I VAL* 4.1 0.3 - - - +
350I PHE* 3.9 2.0 - - - -
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Residues in contact with MET 118 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71I MET* 3.3 1.6 - - - -
72I LYS* 2.8 51.8 + - + +
74I LEU* 4.1 15.7 - - + -
88I THR* 5.2 1.6 - - - +
91I GLU* 3.4 40.2 - - + +
92I LYS* 3.9 29.8 - - + -
95I LEU* 4.1 4.5 - - - -
106I LEU* 3.6 16.4 - - + -
108I PHE 3.6 3.1 - - - -
109I SER* 4.1 4.5 - - - -
117I TYR* 1.3 80.1 - - - +
119I VAL* 1.3 63.0 + - - +
120I MET* 3.3 5.4 - - - +
350I PHE* 4.0 17.0 - - + -
351I G98 4.1 12.8 - - + -
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Residues in contact with VAL 119 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43I PHE* 4.0 21.1 - - + -
60I VAL* 4.7 2.0 - - + -
69I TYR* 3.5 32.8 - - + -
70I ALA 3.4 5.4 - - - +
71I MET* 3.9 26.5 - - + -
106I LEU* 3.6 2.5 - - - +
107I GLU* 2.6 31.8 + - - -
108I PHE* 2.8 37.8 + - + +
110I PHE* 4.1 15.9 - - + -
118I MET* 1.3 74.3 - - - +
120I MET* 1.3 56.1 + - - +
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Residues in contact with MET 120 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57I VAL* 4.7 3.6 - - + -
69I TYR* 3.4 8.1 - - - +
70I ALA* 2.9 52.7 + - + +
71I MET 4.0 0.2 - - - -
72I LYS* 3.5 21.3 - - + +
104I VAL* 4.8 3.6 - - + -
105I LYS 3.1 18.2 - - - +
106I LEU* 4.2 6.1 - - + -
107I GLU* 4.0 7.2 - - - +
118I MET 3.3 21.8 - - - +
119I VAL* 1.3 74.2 - - - +
121I GLU* 1.3 75.3 + - - +
122I TYR 3.4 0.7 + - - -
351I G98 3.5 61.7 - - + +
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Residues in contact with GLU 121 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69I TYR* 4.7 4.5 - - - -
103I LEU 3.7 2.6 - - - +
104I VAL* 3.5 5.9 - - + +
105I LYS* 2.9 53.6 + - + +
107I GLU* 3.6 20.4 - - - +
120I MET* 1.3 74.4 - - - +
122I TYR* 1.3 62.3 + - - +
123I VAL* 4.0 6.2 + - + +
181I GLN* 2.9 24.5 - - - +
351I G98 3.0 26.2 + - - -
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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