Contacts of the helix formed by residues 121 - 125 (chain A) in PDB entry 2BT4
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 TYR 121 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A SER 2.7 12.1 + - - +
85A HIS 3.5 26.2 - - - -
86A THR* 4.0 8.3 - - - -
87A SER 3.9 27.6 - - - +
88A VAL* 3.5 31.8 - - + +
91A LEU* 3.4 17.8 - - + +
119A HIS* 3.7 20.9 - + - -
120A SER* 1.3 69.6 - - - +
122A VAL* 1.3 63.0 + - + +
124A GLN* 3.1 32.2 + - - +
486C THR* 5.5 2.4 - - + +
516C PHE* 3.8 36.1 - + + +
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Residues in contact with VAL 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ILE* 4.3 6.7 - - + -
80A PRO* 3.7 26.9 - - + -
83A TYR 4.9 2.7 - - - +
84A SER* 4.3 7.6 - - - +
87A SER 5.2 0.7 - - - +
90A ILE* 4.0 23.1 - - + -
91A LEU* 4.7 9.2 - - - +
94A LEU* 3.8 20.2 - - + -
104A GLU* 3.7 27.6 - - + +
120A SER* 3.1 8.4 + - - +
121A TYR* 1.3 78.4 - - + +
123A SER* 1.3 58.1 + - - +
124A GLN 3.0 0.2 - - - -
125A ARG* 3.0 5.7 + - - +
126A ALA* 2.9 26.9 + - + +
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Residues in contact with SER 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A GLU* 2.4 25.4 + - - -
120A SER* 3.2 23.4 + - - -
121A TYR 3.2 0.8 - - - -
122A VAL* 1.3 75.7 - - - +
124A GLN* 1.3 61.2 + - - +
125A ARG 3.2 1.0 + - - -
126A ALA* 3.8 1.5 - - - +
129A VAL* 3.7 20.8 - - - +
2413A GOL 4.4 1.8 + - - -
709D ASN* 3.1 25.6 + - - +
711D HIS* 3.8 27.2 + - - +
712D GLN* 3.6 4.3 - - - +
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Residues in contact with GLN 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A LEU* 3.7 15.2 - - + +
95A ASN* 5.3 0.3 - - - +
119A HIS* 3.5 25.1 + - - -
120A SER 4.3 3.6 - - - +
121A TYR* 3.3 21.3 - - - +
122A VAL 3.0 0.6 - - - -
123A SER* 1.3 78.5 - - - +
125A ARG* 1.3 55.5 + - - +
2413A GOL 5.0 4.2 - - - -
514C GLU* 5.2 5.3 - - - +
516C PHE* 3.2 33.0 - - - -
711D HIS 4.4 12.8 - - - +
712D GLN* 2.8 23.2 + - - +
718D HIS* 6.0 3.1 - - + -
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Residues in contact with ARG 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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91A LEU* 3.6 13.9 - - + +
94A LEU* 3.4 36.3 + - + -
95A ASN* 3.4 31.2 + - - +
97A CYS 2.9 29.1 + - - -
98A ASP* 4.8 0.8 - - - +
99A GLY 4.3 4.0 - - - +
100A LEU 2.9 20.0 + - - +
102A VAL* 3.8 15.1 - - + +
122A VAL 3.0 4.8 + - - +
124A GLN* 1.3 78.8 - - - +
126A ALA* 1.3 70.6 + - - +
127A ASP* 3.2 27.8 + - - +
712D GLN* 3.5 7.2 + - - +
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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