Contacts of the strand formed by residues 121 - 127 (chain A) in PDB entry 2BG9
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 PRO 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A VAL 3.9 2.7 - - - +
55A ARG* 4.4 18.8 - - + +
101A ALA 3.6 0.3 - - - +
102A ILE* 3.1 18.7 - - - +
106A THR* 4.4 7.0 - - + -
119A THR 3.7 6.0 - - - +
120A PRO* 1.3 84.5 - - + +
122A ALA* 1.3 61.0 + - - +
149B TYR* 2.7 81.9 - - + +
150B THR* 5.3 1.3 - - - -
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Residues in contact with ALA 122 (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 ILE* 4.9 0.3 - - - +
53A ASN* 3.3 10.5 - - - +
54A VAL* 2.3 73.7 + - + +
56A LEU* 5.0 2.9 - - + +
100A PHE* 4.7 9.4 - - + -
101A ALA 3.1 18.6 - - - +
102A ILE* 4.8 0.4 - - - -
103A VAL* 4.8 9.4 - - + -
120A PRO 2.9 8.5 + - - +
121A PRO* 1.3 75.0 - - - +
123A ILE* 1.2 56.3 - - - +
149B TYR* 4.4 1.0 + - - -
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Residues in contact with ILE 123 (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 ILE* 3.4 35.0 - - + -
51A GLU* 4.6 6.3 - - + +
52A THR* 2.6 30.5 - - - +
53A ASN* 3.6 21.3 - - - +
54A VAL* 4.1 0.4 - - - +
101A ALA* 2.6 51.0 + - + +
102A ILE* 4.8 10.8 - - + -
122A ALA* 1.2 76.3 - - - +
124A PHE* 1.3 56.7 + - - +
97B ASP* 5.8 1.3 - - - +
149B TYR* 5.8 0.9 - - + +
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Residues in contact with PHE 124 (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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35A LEU* 5.6 4.5 - - + -
37A LEU* 5.7 0.9 - - + -
50A VAL 3.4 0.2 - - - +
51A GLU* 3.0 11.6 - - - +
52A THR* 2.9 46.7 + - - -
54A VAL* 4.3 11.2 - - + -
92A LEU* 3.5 40.8 - - + -
96A ALA* 6.0 0.7 - - - -
98A GLY 4.5 6.5 - - - -
99A ASP 3.4 19.7 - - - +
100A PHE* 3.2 41.1 - + + -
101A ALA* 4.1 1.3 - - - +
123A ILE* 1.3 74.5 - - - +
125A LYS* 1.4 72.1 + - - +
126A SER* 2.9 26.5 - - - -
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Residues in contact with LYS 125 (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 ILE* 4.2 25.0 - - + +
50A VAL 3.5 2.0 - - - +
51A GLU* 3.9 32.6 + - + +
96A ALA* 4.2 1.4 - - - -
97A ASP* 3.9 12.1 + - + +
98A GLY* 3.1 41.3 + - - +
99A ASP 4.5 2.2 + - - +
124A PHE* 1.4 82.3 - - - +
126A SER* 1.3 61.3 + - - +
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Residues in contact with SER 126 (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 ILE* 3.2 13.0 - - - +
50A VAL* 2.7 44.7 + - - -
52A THR* 4.0 7.2 + - - +
92A LEU* 5.7 0.7 - - - -
95A ASN* 5.1 2.9 - - - -
96A ALA 5.1 0.7 - - - +
97A ASP* 4.2 5.5 - - - +
124A PHE* 2.9 30.2 - - - -
125A LYS* 1.3 72.9 - - - +
127A TYR* 1.3 65.4 - - - +
128A CYS 4.2 0.2 - - - -
144A MET* 4.1 20.9 - - - -
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Residues in contact with TYR 127 (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 ASN 4.8 3.8 - - - -
48A GLN* 3.4 40.1 + - + -
49A ILE* 5.0 1.6 - - + -
94A ASN* 2.7 34.0 + - - +
95A ASN* 2.9 43.8 - - - +
97A ASP* 3.7 31.0 - - + -
126A SER* 1.3 82.2 - - - +
128A CYS* 1.3 57.8 + - - +
144A MET* 4.3 0.2 - - - -
37E THR 5.9 0.9 - - - -
38E ASN* 3.0 41.5 + - + -
40E ILE* 5.5 5.7 - - + -
178E THR* 4.4 10.4 + - - +
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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