Contacts of the strand formed by residues 135 - 139 (chain A) in PDB entry 1MVL
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 LEU 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A LEU* 3.3 31.6 - - + +
102A ILE* 4.2 11.4 - - + -
113A ILE* 6.0 0.4 - - + -
126A ILE* 4.4 10.5 - - + -
129A TRP* 3.8 24.2 - - + +
131A TYR* 3.8 28.7 - - + +
133A LYS 3.5 1.0 + - - +
134A PRO* 1.3 76.4 - - - +
136A PHE* 1.3 68.0 + - - +
137A VAL* 3.7 25.8 - - + -
162A GLY 5.3 2.4 + - - -
163A ILE* 3.4 24.0 - - + +
164A THR* 2.9 26.5 + - - -
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Residues in contact with PHE 136 (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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99A VAL* 3.8 19.5 - - + -
100A LEU 2.8 8.6 + - - +
101A VAL* 3.3 10.1 - - + -
102A ILE 2.8 24.6 + - - -
134A PRO* 3.9 21.5 - - + -
135A LEU* 1.3 78.2 - - - +
137A VAL* 1.3 67.8 + - - +
164A THR* 3.3 41.3 - - + +
166A ILE* 4.1 17.0 - - + -
192A THR* 3.9 26.0 - - + -
193A VAL* 3.8 24.0 - - + -
196A PHE* 3.9 35.9 - + + -
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Residues in contact with VAL 137 (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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101A VAL* 5.9 0.2 - - - -
102A ILE* 3.4 19.5 - - + +
105A LEU* 3.6 31.0 - - + -
113A ILE* 5.1 0.7 - - + -
135A LEU* 3.7 18.4 - - + -
136A PHE* 1.3 80.8 - - - +
138A ALA* 1.3 57.7 + - - +
139A PRO* 3.5 3.4 - - + +
155A LEU* 5.0 2.7 - - + -
158A LEU* 4.4 10.1 - - + -
163A ILE* 3.8 21.5 - - + -
164A THR 2.9 10.1 + - - +
165A LEU* 4.2 16.4 - - + -
166A ILE* 2.8 33.6 + - - +
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Residues in contact with ALA 138 (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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101A VAL* 5.9 0.2 - - + -
102A ILE 2.8 7.5 + - - -
103A ALA* 3.5 25.1 - - + -
104A PRO* 3.6 5.2 - - - +
105A LEU* 3.1 19.0 + - - -
137A VAL* 1.3 73.0 - - - +
139A PRO* 1.3 68.3 - - - +
140A ALA 3.6 0.2 + - - -
166A ILE* 3.6 13.0 - - + +
183A MET* 3.9 9.9 - - + +
184A ALA* 4.8 2.2 - - + -
189A ILE* 3.7 22.4 - - + -
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Residues in contact with PRO 139 (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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105A LEU* 3.4 22.0 - - + +
110A LEU* 5.8 0.4 - - + -
137A VAL* 3.5 3.1 - - + +
138A ALA* 1.3 85.5 - - - +
140A ALA* 1.3 61.2 + - - +
141A MET* 4.2 13.2 - - + -
146A TRP* 3.8 23.1 - - + -
155A LEU* 4.2 17.0 - - + -
165A LEU* 3.3 34.3 - - + -
166A ILE 3.4 6.5 - - - +
168A PRO* 3.8 11.9 - - + +
181A GLY 3.8 4.4 - - - +
183A MET* 3.7 13.0 - - - -
184A ALA 4.6 0.5 + - - -
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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