Contacts of the strand formed by residues 128 - 133 (chain A) in PDB entry 6MVL
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 ASN 128 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A THR* 4.6 9.5 + - - +
54A CYS 3.5 6.8 - - - +
55A ARG* 3.8 17.7 - - - +
70A LYS* 5.1 0.5 + - - -
123A SER* 3.4 2.3 - - - -
124A ASP* 2.8 56.8 + - + +
126A HIS* 3.1 21.2 + - - +
127A GLY* 1.3 77.3 - - - +
129A PHE* 1.3 61.5 + - - +
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Residues in contact with PHE 129 (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 VAL* 4.7 1.3 - - + -
53A THR* 3.5 1.5 + - - -
54A CYS* 2.9 55.5 + - + +
55A ARG 4.5 1.3 - - - -
56A LEU* 4.6 5.8 - - + -
70A LYS* 3.7 29.4 - - + -
71A THR 3.8 11.0 - - - -
72A TRP* 3.5 26.0 - + - -
99A LEU* 3.8 14.4 - - + -
122A ALA 3.4 11.2 - - - +
123A SER* 4.1 4.3 - - - +
127A GLY 3.8 9.6 - - - -
128A ASN* 1.3 75.1 - - - +
130A SER* 1.3 63.6 + - - +
146A CYS* 3.6 33.4 - - + -
147A LEU 4.3 0.9 - - - -
148A VAL* 3.5 33.7 - - + -
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Residues in contact with SER 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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51A THR* 3.7 21.1 - - - +
52A LEU 3.0 19.3 - - - -
53A THR* 4.2 6.7 - - - -
72A TRP* 3.5 12.6 + - - +
120A GLU 3.8 0.6 - - - +
121A SER* 3.4 4.0 + - - -
122A ALA* 2.8 52.8 + - - +
123A SER* 5.5 0.2 - - - -
129A PHE* 1.3 74.8 - - - +
131A ILE* 1.3 57.5 + - - +
132A THR* 4.3 1.8 + - - -
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Residues in contact with ILE 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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50A VAL 3.8 1.0 - - - +
51A THR* 3.4 1.2 - - - -
52A LEU* 2.9 52.9 + - + +
72A TRP* 3.5 39.0 - - + +
89A ILE* 5.0 7.2 - - + -
97A LEU* 4.0 38.4 - - + -
119A LEU* 4.4 17.0 - - + -
120A GLU 3.4 11.4 - - - +
121A SER* 4.1 15.0 - - - +
130A SER* 1.3 74.4 - - - +
132A THR* 1.3 68.8 + - - +
133A MET* 4.0 5.7 + - + -
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Residues in contact with THR 132 (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 ASN* 4.9 7.2 - - + +
50A VAL 3.3 11.4 - - - +
51A THR* 2.8 28.7 + - - +
118A GLY 3.5 0.7 - - - +
119A LEU* 3.3 11.3 - - - +
120A GLU* 2.8 46.4 + - + -
130A SER* 4.3 1.8 + - - -
131A ILE* 1.3 70.1 - - - +
133A MET* 1.3 61.6 + - - +
134A ARG* 4.0 20.4 - - + +
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Residues in contact with MET 133 (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 ASN* 3.4 2.4 - - - -
50A VAL* 2.8 38.1 + - + +
52A LEU* 4.1 12.3 - - + -
89A ILE* 3.9 16.4 - - + -
90A ARG* 3.9 9.0 - - - +
118A GLY 3.5 4.5 - - - -
119A LEU* 3.7 12.1 - - + -
131A ILE* 4.6 12.8 - - + +
132A THR* 1.3 73.7 - - - +
134A ARG* 1.3 62.1 + - - +
136A LEU* 3.8 15.3 - - + +
140A ASP* 3.6 28.0 - - + +
144A TYR* 3.3 42.6 - - + +
166A LEU* 4.1 11.9 - - - -
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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