Contacts of the strand formed by residues 99 - 105 (chain A) in PDB entry 3S3J
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 99 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A THR* 4.0 14.8 - - + +
43A LEU 3.3 8.1 - - - -
44A HIS* 4.6 18.4 - - + +
49A ASN* 3.1 9.3 + - - -
94A ASP* 5.1 1.7 + - - -
95A GLN* 3.5 2.8 - - - -
96A GLN* 3.0 44.8 + - + +
97A ASP* 3.7 0.4 - - + -
98A CYS* 1.3 88.3 - - + +
100A LEU* 1.3 61.2 + - - +
101A SER* 4.6 4.9 + - - -
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Residues in contact with LEU 100 (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 LEU 3.9 0.3 - - - +
42A THR* 3.4 1.8 - - - -
43A LEU* 2.9 44.4 + - + +
45A PHE* 4.0 21.5 - - + -
49A ASN* 4.0 2.9 - - - +
50A TYR* 3.4 38.1 - - + -
57A LEU* 4.9 0.4 - - + -
79A LEU* 4.2 8.3 - - + -
92A VAL* 3.6 21.8 - - + -
94A ASP 3.7 0.4 - - - -
95A GLN* 3.6 36.3 - - + +
99A THR* 1.3 73.9 - - - +
101A SER* 1.3 60.8 + - - +
102A LEU* 3.8 22.8 + - + +
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Residues in contact with SER 101 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A TRP* 6.5 0.2 - - - -
41A LEU 3.5 5.8 - - - -
42A THR* 3.4 23.3 + - - +
92A VAL* 3.7 3.8 - - - +
93A VAL* 3.0 31.3 + - - -
94A ASP* 2.8 42.0 + - - +
99A THR* 4.2 3.9 + - - -
100A LEU* 1.3 71.6 - - - +
102A LEU* 1.3 62.8 + - - +
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Residues in contact with LEU 102 (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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40A TRP* 3.5 9.0 - - - +
41A LEU* 2.8 49.4 + - + +
43A LEU* 3.9 14.4 - - + -
59A PHE* 3.4 35.9 - - + -
79A LEU* 3.6 24.7 - - + -
91A THR 3.3 7.2 - - - +
92A VAL* 4.1 4.7 - - + -
93A VAL* 4.5 4.2 - - - +
100A LEU* 3.8 31.4 - - + +
101A SER* 1.3 82.3 - - - +
103A GLN* 1.3 61.1 + - - +
104A LEU* 3.9 12.6 - - + -
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Residues in contact with GLN 103 (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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38A PRO* 3.7 31.6 - - + +
39A PHE 3.3 6.3 - - - +
40A TRP* 2.8 26.3 + - + +
89A THR* 3.9 1.2 + - - +
90A ALA* 3.3 3.6 - - - -
91A THR* 2.9 40.5 + - + +
93A VAL* 3.8 26.5 - - + +
102A LEU* 1.3 75.5 - - - +
104A LEU* 1.3 64.6 + - - +
105A THR* 4.7 3.9 + - - +
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Residues in contact with LEU 104 (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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38A PRO* 3.1 2.8 - - - +
39A PHE* 2.7 71.4 + - + +
41A LEU* 3.9 32.3 - - + -
59A PHE* 4.6 5.4 - - + -
61A VAL* 5.9 0.7 - - + -
77A PHE* 4.2 18.4 - - + -
88A TRP* 6.2 2.7 - - + -
89A THR 3.2 11.9 - - - +
90A ALA* 4.0 11.4 - - + -
102A LEU* 3.9 20.2 - - + -
103A GLN* 1.3 79.7 - - - +
105A THR* 1.3 65.1 + - - +
106A THR* 6.1 0.2 - - + -
117A LEU* 4.2 20.0 - - + -
135A PHE* 6.0 0.2 - - + -
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Residues in contact with THR 105 (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 GLY 4.1 4.3 - - - +
37A GLN 3.7 9.2 - - - +
38A PRO* 3.7 34.0 - - + +
83A VAL* 5.4 4.6 - - - +
86A GLY 6.3 0.7 - - - +
87A ASP 3.9 5.4 - - - +
88A TRP* 3.2 10.6 - - - -
89A THR* 3.0 41.2 + - - +
103A GLN* 4.7 4.2 + - - +
104A LEU* 1.3 78.4 + - - +
106A THR* 1.3 78.4 + - - +
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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