Contacts of the strand formed by residues 97 - 103 (chain T) in PDB entry 2P8Z
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 SER 97 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12T LEU* 4.3 14.3 - - - +
15T LYS* 6.0 6.1 - - - +
18T ASN* 2.8 32.9 + - - +
78T TYR* 2.6 33.9 + - - -
79T SER 3.5 4.0 - - - -
80T GLU* 3.8 5.4 + - - +
94T ASP 5.0 0.8 + - - +
95T GLY* 3.6 1.2 - - - -
96T ASN* 1.3 75.6 - - - +
98T PHE* 1.3 63.8 + - - +
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Residues in contact with PHE 98 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12T LEU* 5.2 2.0 - - - -
17T THR 5.0 0.4 - - - -
18T ASN* 3.0 46.7 - - + +
20T ARG* 4.1 19.7 - - + -
77T LEU 3.8 0.2 - - - +
78T TYR* 3.5 11.9 - - - -
79T SER* 2.7 41.8 + - - +
81T MET* 3.7 15.9 - - + -
86T VAL* 4.2 2.0 - - + -
89T ILE* 3.6 20.6 - - + -
93T THR* 3.9 12.3 - - + -
95T GLY 4.0 2.0 - - - -
96T ASN* 3.4 24.7 - - - -
97T SER* 1.3 73.5 - - - +
99T LEU* 1.3 60.1 + - - +
100T ILE* 4.0 6.2 - - + +
339T VAL* 3.7 39.9 - - + -
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Residues in contact with LEU 99 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9T MET* 4.6 9.0 - - + -
12T LEU* 4.1 27.1 - - + +
13T MET* 3.9 28.3 - - + +
18T ASN 2.9 10.1 + - - +
19T VAL* 3.2 21.0 - - + +
20T ARG* 2.9 24.9 + - - +
45T ILE* 3.7 20.2 - - + -
76T SER* 4.1 15.0 - - - +
77T LEU 3.5 14.8 - - - +
78T TYR* 5.0 0.2 - - - +
98T PHE* 1.3 72.3 - - - +
100T ILE* 1.3 62.9 + - - +
101T ASN* 4.5 17.0 - - - +
452T ASN* 5.9 0.4 - - - +
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Residues in contact with ILE 100 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20T ARG* 3.5 20.4 - - + +
22T MET* 4.2 17.3 - - + -
75T ILE 3.5 1.7 - - - +
76T SER* 3.4 4.0 - - - -
77T LEU* 2.7 61.2 + - + +
79T SER* 4.4 9.6 - - - -
98T PHE* 4.7 3.1 - - + -
99T LEU* 1.3 81.7 - - - +
101T ASN* 1.3 64.2 + - - +
102T LEU 3.6 0.4 + - - +
335T LEU* 3.8 26.9 - - + -
338T ILE* 3.8 29.6 - - + -
339T VAL* 4.2 15.9 - - + -
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Residues in contact with ASN 101 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69S GLU* 5.2 0.2 - - - +
19T VAL* 3.9 10.0 - - - +
20T ARG 2.8 8.6 + - - +
21T ASN* 2.8 31.5 + - - +
22T MET* 3.0 28.8 + - - +
74T ALA* 5.8 4.7 - - + +
75T ILE 3.6 4.1 + - - +
76T SER* 3.8 20.4 + - - +
99T LEU* 4.5 14.2 - - - +
100T ILE* 1.3 74.9 - - - +
102T LEU* 1.3 59.3 - - - +
103T ILE* 3.4 12.7 + - + +
453T ILE* 5.2 11.1 + - + +
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Residues in contact with LEU 102 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68S VAL* 2.2 60.4 + - + +
22T MET* 3.1 39.5 - - + +
23T SER* 4.9 1.3 - - - -
24T VAL* 3.9 16.2 - - + +
36T THR* 3.8 25.8 - - + +
39T LEU* 4.0 23.3 - - + -
74T ALA* 3.4 1.6 - - - -
75T ILE* 2.8 17.4 + - + +
77T LEU* 4.7 15.3 - - + -
100T ILE 3.6 1.8 + - - -
101T ASN* 1.3 69.1 - - - +
103T ILE* 1.3 63.5 + - - +
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Residues in contact with ILE 103 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67S HIS* 3.8 11.4 - - + +
68S VAL 5.3 0.2 - - - -
21T ASN* 4.6 6.1 - - + -
22T MET 2.8 17.4 + - - +
23T SER* 3.2 22.2 - - - -
24T VAL 4.6 1.2 + - - -
73T THR 4.1 2.5 - - - +
74T ALA* 4.3 8.7 - - + -
101T ASN* 3.9 14.8 - - + +
102T LEU* 1.3 75.2 - - - +
104T ASP* 1.3 75.0 + - - +
105T SER* 3.6 0.7 + - - -
118T ALA* 4.4 4.9 - - + +
121T VAL* 3.7 36.6 - - + +
122T THR* 3.6 27.6 - - + -
397T PHE* 4.5 8.7 - - + -
453T ILE* 4.3 16.2 - - + -
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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