Contacts of the strand formed by residues 127 - 131 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B VAL* 3.3 9.0 - - + +
109B HIS* 4.7 13.7 - - + +
116B ALA 5.2 1.3 - - - +
117B ARG* 5.5 3.8 - - - +
120B ALA* 3.6 23.8 - - + -
125B VAL 3.5 1.6 + - - +
126B PRO* 1.3 73.4 - - - +
128B VAL* 1.3 67.3 + - - +
129B SER 4.2 0.4 - - - -
186B PRO* 4.8 15.9 - - + +
187B ARG* 3.8 17.2 - - - +
396B GLU* 6.1 0.2 - - - -
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Residues in contact with VAL 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B LEU* 4.4 12.3 - - + -
107B VAL 2.8 9.2 + - - +
108B LEU* 3.4 25.0 - - + +
109B HIS* 3.1 28.3 + - - -
127B ALA* 1.3 79.6 - - - +
129B SER* 1.3 71.4 + - - +
130B LEU* 4.2 0.7 - - + -
187B ARG* 3.8 15.5 - - + +
189B LEU* 4.1 25.1 - - + +
393B ILE* 4.5 6.3 - - + -
396B GLU* 3.9 33.2 - - + -
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Residues in contact with SER 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B HIS* 3.4 28.5 + - - -
111B ILE* 3.7 22.9 - - - +
117B ARG* 5.4 1.4 + - - -
127B ALA 4.2 0.4 - - - -
128B VAL* 1.3 74.3 - - - +
130B LEU* 1.3 62.9 + - - +
131B SER 4.0 0.2 - - - -
185B PRO* 3.8 25.5 - - - +
187B ARG 3.0 16.3 + - - -
188B SER* 3.2 5.4 + - - -
189B LEU 2.9 26.0 + - - -
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Residues in contact with LEU 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B MET* 4.1 7.9 - - + -
23B SER* 3.6 30.3 - - - +
26B VAL* 5.1 8.1 - - + -
27B ILE* 5.2 0.2 - - + -
108B LEU* 3.6 46.7 - - + -
109B HIS 2.8 14.7 + - - +
110B ASP* 3.4 27.8 - - - +
111B ILE 3.5 3.6 + - - -
128B VAL* 4.2 0.7 - - + -
129B SER* 1.3 75.6 + - - +
131B SER* 1.3 60.8 + - - +
189B LEU* 3.5 35.7 - - + -
191B LEU* 3.9 15.0 - - + -
389B ALA* 6.0 0.9 - - + -
393B ILE* 4.5 2.2 - - + -
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Residues in contact with SER 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B ILE* 3.8 17.2 - - - +
129B SER 4.0 0.6 - - - -
130B LEU* 1.3 72.8 - - - +
132B PRO* 1.3 63.3 - - - +
133B ASN* 2.7 32.4 + - - +
134B LEU 3.8 2.8 + - - -
135B VAL* 3.6 23.6 - - - +
188B SER* 4.4 4.9 - - - -
189B LEU 2.9 13.5 + - - -
190B VAL* 3.7 1.9 - - - -
191B LEU* 2.8 35.3 + - - +
501B ERY 5.9 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
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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