Contacts of the strand formed by residues 68 - 74 (chain A) in PDB entry 2P18
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 THR 68 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A THR 5.4 1.6 + - - -
35A HIS 2.9 13.6 + - - -
36A THR* 3.3 12.4 - - + +
37A LEU* 2.7 33.2 + - - -
66A THR 5.5 0.3 + - - -
67A TYR* 1.4 73.3 + - - +
69A PHE* 1.3 55.7 + - - +
70A SER* 3.4 21.7 + - - +
99A VAL 5.3 10.8 - - - +
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Residues in contact with PHE 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LEU* 4.1 7.2 - - + -
37A LEU* 3.5 23.1 - - + -
38A ALA 4.0 2.0 - - - -
39A ALA* 3.6 30.3 - - + -
49A ILE* 4.5 5.8 - - + -
50A LEU* 4.7 5.2 - - + -
53A ILE* 3.6 32.1 - - + -
67A TYR 4.1 1.6 + - - -
68A THR* 1.3 73.6 - - - +
70A SER* 1.3 58.7 + - - +
71A THR 3.6 21.1 - - - -
72A ILE* 4.9 0.9 - - + -
88A LEU* 4.0 14.6 - - + -
92A LEU* 3.8 38.3 - - + +
99A VAL 3.9 7.8 + - - +
101A VAL* 3.8 17.8 - - - +
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Residues in contact with SER 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A THR* 3.4 25.6 - - - +
37A LEU 3.0 6.9 + - - -
68A THR* 3.4 13.9 + - - -
69A PHE* 1.3 74.7 - - - +
71A THR* 1.3 73.5 + - - +
99A VAL 5.1 2.0 - - - +
100A PRO 3.5 10.3 - - - +
101A VAL* 3.4 7.7 - - - -
102A VAL* 2.8 26.3 + - - +
125A GLN 5.3 0.2 + - - -
126A VAL* 4.8 3.6 - - - +
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Residues in contact with THR 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A LEU 3.7 2.0 + - - -
38A ALA* 3.2 15.3 - - - -
39A ALA 3.0 23.4 + - - -
69A PHE* 3.6 7.9 - - - -
70A SER* 1.3 94.1 + - - +
72A ILE* 1.3 65.8 + - - +
73A LEU* 3.6 28.3 - - + -
101A VAL* 5.0 0.7 - - - -
102A VAL* 3.2 18.8 - - + +
104A VAL* 3.9 15.9 - - + -
116A LYS* 5.7 1.0 + - - -
124A VAL* 5.3 2.5 - - + -
125A GLN 4.3 6.8 + - - +
126A VAL* 4.2 13.0 - - + +
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Residues in contact with ILE 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ALA* 3.4 11.2 - - + +
42A VAL* 4.0 13.9 - - + +
69A PHE* 4.9 0.4 - - + -
71A THR* 1.3 77.5 - - - +
73A LEU* 1.3 64.1 + - - +
74A SER* 4.6 0.7 - - - +
85A ASN* 3.5 50.0 - - - +
88A LEU* 4.1 22.9 - - + -
89A LYS* 4.0 14.8 - - + +
92A LEU* 4.5 4.0 - - + -
101A VAL* 4.1 19.3 - - + -
102A VAL 2.7 11.9 + - - +
103A VAL* 3.3 9.8 - - + +
104A VAL* 2.7 32.9 + - - +
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Residues in contact with LEU 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ILE* 4.4 5.8 - - + -
38A ALA* 3.9 17.0 - - + -
39A ALA 2.8 18.7 + - - +
40A VAL* 3.3 17.0 - - + +
41A ASP* 2.8 26.2 + - - +
71A THR* 3.6 21.8 - - + -
72A ILE* 1.3 79.0 - - - +
74A SER* 1.3 62.0 + - - +
104A VAL* 3.5 23.8 - - + -
124A VAL* 4.4 4.5 - - + -
126A VAL* 4.7 2.9 - - + -
131A VAL* 3.9 29.2 - - + -
146A TYR* 3.8 26.2 - - + -
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Residues in contact with SER 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ASP* 3.4 4.7 + - - +
72A ILE* 4.6 1.2 - - - +
73A LEU* 1.3 75.2 + - - +
75A THR* 1.3 63.4 + - - +
76A HIS 3.5 6.7 + - - -
81A HIS 4.0 8.7 + - - -
82A SER* 4.8 0.4 - - - -
85A ASN* 2.9 33.8 + - - -
103A VAL* 4.8 0.2 - - - +
104A VAL 2.9 12.4 + - - +
105A GLY* 3.9 1.0 - - - -
111A ILE* 3.6 33.4 - - - +
144A VAL* 4.2 1.4 - - - +
146A TYR* 2.7 23.5 + - - -
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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