Contacts of the strand formed by residues 101 - 106 (chain A) in PDB entry 8ATC
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 ALA 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A VAL 4.2 1.6 + - - -
44A ILE* 3.7 18.7 - - + +
45A ALA 3.2 21.1 + - - -
99A VAL* 3.4 9.2 - - - +
100A ASP* 1.3 74.4 - - - +
102A ILE* 1.3 63.0 + - - +
103A VAL 4.2 0.4 - - - -
122A VAL* 4.1 0.9 - - - -
123A PRO* 3.4 13.0 - - + +
125A LEU* 3.9 21.1 - - + -
300A LEU* 4.8 1.8 - - + -
303A VAL* 5.4 0.4 - - + -
304A LEU* 4.2 21.8 - - + -
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Residues in contact with ILE 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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45A ALA* 3.6 4.9 - - + -
47A CYS* 4.6 15.3 - - - -
92A ILE* 4.2 24.9 - - + -
95A ILE* 4.2 9.2 - - + -
96A SER* 4.1 21.8 - - - +
99A VAL* 3.7 18.6 - - + -
101A ALA* 1.3 75.6 - - - +
103A VAL* 1.3 65.9 - - - +
104A MET* 4.3 11.4 - - + -
119A SER* 4.2 12.6 - - - -
122A VAL* 3.9 17.0 - - + -
123A PRO 3.0 7.8 + - - +
124A VAL* 3.3 13.7 - - + +
125A LEU* 2.7 32.9 + - - +
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Residues in contact with VAL 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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44A ILE* 4.1 6.7 - - + -
45A ALA 2.9 11.9 + - - +
46A SER* 4.4 3.1 - - - -
47A CYS* 2.9 26.7 + - - +
48A PHE* 4.2 11.4 - - + -
59A PHE* 3.7 44.4 - - + -
63A MET* 3.7 27.4 - - + -
102A ILE* 1.3 73.6 - - - +
104A MET* 1.3 65.2 + - - +
125A LEU* 3.5 19.1 - - + +
127A ALA* 3.9 11.7 - - + -
300A LEU* 4.8 1.6 - - + -
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Residues in contact with MET 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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47A CYS* 3.1 18.2 - - + +
48A PHE* 5.4 0.2 - - - -
49A PHE* 3.6 16.6 - - + -
88A LEU* 3.2 46.7 - - + -
92A ILE* 4.4 7.9 - - + -
102A ILE* 4.3 9.2 - - + -
103A VAL* 1.3 77.0 - - - +
105A ARG* 1.3 57.6 + - - +
106A HIS* 3.8 16.6 - - + -
111A ALA* 4.2 7.6 - - - +
112A ALA* 4.5 10.8 - - + +
115A ALA* 4.1 22.9 - - - -
124A VAL* 4.9 5.4 - - + -
125A LEU 3.0 12.5 + - - +
126A ASN* 3.7 5.8 - - - +
127A ALA* 2.8 26.5 + - - -
128A GLY 3.9 1.2 + - - +
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Residues in contact with ARG 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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47A CYS 3.1 4.8 + - - -
48A PHE* 3.4 33.0 - - + +
49A PHE* 2.7 35.8 + - - -
50A GLU* 3.7 25.6 - - + +
51A ALA 3.2 21.3 + - - -
52A SER* 3.7 1.6 - - - -
55A THR* 2.9 28.9 + - - -
104A MET* 1.3 72.3 - - - +
106A HIS* 1.3 60.4 + - - +
127A ALA* 2.9 26.3 + - + +
128A GLY 3.1 10.5 - - - +
134A HIS* 3.1 7.7 + - - -
167A ARG* 3.4 12.3 - - - +
311A PAL 2.9 49.6 + - - -
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Residues in contact with HIS 106 (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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49A PHE* 3.6 30.2 - + - +
50A GLU* 3.6 10.3 - - - +
81A LEU* 5.7 2.2 - - - +
88A LEU* 4.0 12.7 - - + +
104A MET* 3.8 17.0 - - + -
105A ARG* 1.3 74.4 - - - +
107A PRO* 1.3 71.8 - - + +
108A GLN* 2.9 40.3 + - - -
111A ALA* 3.2 27.4 - - + +
128A GLY 2.8 8.3 + - - +
129A ASP* 3.2 3.8 - - + -
130A GLY 2.9 27.9 + - - -
115B ILE* 3.7 18.4 - - + -
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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