Contacts of the strand formed by residues 521 - 525 (chain A) in PDB entry 1MVM
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 THR 521 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A MET* 3.3 23.7 - - - +
152A LEU* 5.2 3.1 - - + -
153A LYS 3.8 14.4 - - - +
154A THR* 4.3 3.3 - - - +
171A ASP* 5.5 1.1 - - + +
174A ALA* 5.1 13.7 - - + -
175A CYS 5.9 0.9 - - - +
501A LEU* 2.8 34.5 - - + +
502A GLY 5.4 4.9 - - - +
504A ASN* 3.2 36.7 + - + +
519A ILE* 2.9 17.0 + - - +
520A VAL* 1.3 77.5 + - - +
522A TYR* 1.3 63.7 + - - +
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Residues in contact with TYR 522 (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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72A HIS* 3.8 20.9 - + - -
73A LEU 3.9 3.6 - - - +
74A ASN* 3.4 28.7 - - - +
151A VAL* 6.2 0.4 - - + -
152A LEU* 3.8 6.2 - - - +
153A LYS* 3.0 59.2 + - + +
155A VAL* 3.4 33.4 - - + -
168A TYR* 3.5 24.8 - + - +
501A LEU* 3.5 11.9 - - - -
520A VAL* 5.6 4.0 - - + -
521A THR* 1.3 75.7 - - - +
523A GLY* 1.4 66.6 + - - +
524A THR* 5.4 5.6 - - + -
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Residues in contact with GLY 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A VAL 3.8 0.9 - - - +
72A HIS* 3.6 4.4 - - - -
73A LEU* 3.0 38.4 + - - +
151A VAL* 3.1 14.4 - - - -
152A LEU* 4.0 8.3 - - - -
153A LYS 4.8 0.2 - - - -
176A MET* 6.2 0.9 - - - -
501A LEU* 4.5 2.6 - - - +
522A TYR* 1.4 84.9 - - - +
524A THR* 1.4 64.7 - - - -
525A PHE* 4.9 3.8 - - - -
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Residues in contact with THR 524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LEU* 4.0 22.7 - - + -
71A VAL 3.3 8.5 - - - +
72A HIS* 4.6 14.6 - - + -
149A ASN 3.6 1.8 + - - +
150A VAL* 3.4 0.8 - - - +
151A VAL* 2.5 79.1 + - + +
176A MET* 5.7 0.2 - - - -
522A TYR* 5.4 6.3 - - + -
523A GLY* 1.4 74.2 - - - +
525A PHE* 1.4 67.6 - - - +
526A PHE* 5.8 1.3 - - - -
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Residues in contact with PHE 525 (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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70A LEU* 4.5 0.2 - - - -
71A VAL* 2.8 61.0 + - + -
73A LEU* 4.4 10.8 - - + -
114A VAL* 4.8 8.1 - - + -
147A ILE* 3.4 24.7 - - + -
148A PHE 3.9 6.5 - - - +
149A ASN 3.8 6.5 - - - -
150A VAL* 4.1 14.8 - - + -
176A MET* 2.2 42.6 - - + -
208A ALA* 6.2 0.7 - - + -
497A MET* 5.7 0.2 - - + -
499A VAL* 3.6 21.8 - - + -
523A GLY 4.9 3.6 - - - -
524A THR* 1.4 82.2 - - - +
526A PHE* 0.9 94.5 + - - +
527A TRP* 4.6 8.1 - + + -
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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