Contacts of the strand formed by residues 127 - 131 (chain A) in PDB entry 4M83
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 127 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A VAL* 3.3 7.9 - - + +
109A HIS* 4.3 18.8 - - + +
116A ALA 5.2 0.4 - - - +
117A ARG* 5.5 3.1 - - - -
120A ALA* 3.6 23.6 - - + -
121A ARG* 6.2 1.8 - - - +
125A VAL 3.6 1.6 + - - +
126A PRO* 1.3 76.4 - - - +
128A VAL* 1.3 64.6 + - - +
129A SER 4.1 0.4 - - - -
186A PRO* 4.9 13.7 - - + +
187A ARG* 4.0 17.7 + - - +
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Residues in contact with VAL 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A LEU* 4.3 10.8 - - + -
107A VAL 2.8 9.7 + - - -
108A LEU* 3.5 19.5 - - + +
109A HIS* 3.1 26.7 + - - -
126A PRO* 5.4 0.9 - - + -
127A ALA* 1.3 76.6 - - - +
129A SER* 1.3 69.3 + - - +
130A LEU* 3.8 15.6 + - + +
187A ARG* 3.8 14.8 - - + +
189A LEU* 4.1 20.2 - - + +
393A ILE* 4.6 5.2 - - + -
396A GLU* 3.8 36.1 - - + -
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Residues in contact with SER 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A HIS* 3.4 29.3 + - - -
111A ILE* 3.6 23.4 - - - +
117A ARG* 5.4 1.2 + - - -
127A ALA 4.1 0.4 - - - -
128A VAL* 1.3 72.5 - - - +
130A LEU* 1.3 62.3 + - - +
131A SER 4.0 0.2 - - - -
185A PRO* 3.8 22.7 - - - +
187A ARG 3.0 15.9 + - - -
188A SER* 3.2 6.9 + - - -
189A LEU 2.9 26.0 + - - -
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Residues in contact with LEU 130 (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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11A MET* 3.9 22.9 - - + -
23A SER* 3.8 30.1 - - - -
26A VAL* 4.5 11.4 - - + -
27A ILE* 5.3 0.2 - - + -
108A LEU* 4.8 10.1 - - + -
109A HIS 2.8 17.8 + - - +
110A ASP* 3.5 7.3 - - + +
111A ILE 3.5 18.4 + - - -
128A VAL* 4.0 17.5 - - + +
129A SER* 1.3 81.1 + - - +
131A SER* 1.3 60.1 + - - +
132A PRO* 3.7 4.9 - - - +
189A LEU* 3.5 28.5 - - + +
191A LEU* 5.1 11.0 - - + -
389A ALA* 6.3 0.4 - - + -
393A ILE* 4.4 7.6 - - + -
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Residues in contact with SER 131 (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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111A ILE* 3.9 16.5 - - - +
129A SER 4.0 0.6 - - - -
130A LEU* 1.3 71.5 - - - +
132A PRO* 1.3 59.5 - - - +
133A ASN* 2.7 39.0 + - - -
134A LEU 3.8 0.5 + - - -
135A VAL* 3.7 22.3 - - - +
188A SER* 4.3 5.2 - - - -
189A LEU 2.9 12.8 + - - -
190A VAL* 3.6 3.0 - - - +
191A LEU* 2.8 34.5 + - - +
1400A ERY 6.0 0.2 - - - +
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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
------------------------------------------------------------
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