Contacts of the strand formed by residues 8 - 12 (chain 7) in PDB entry 1MVW
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 8 (chain 7).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77 ALA* 1.3 77.0 - - - +
97 VAL* 1.3 68.2 + - - +
107 CYS* 4.1 1.3 - - + -
207 GLY 3.6 3.8 - - - +
217 PHE* 3.5 36.1 - - + -
907 PHE* 4.0 25.6 - - + -
947 LEU* 4.2 14.1 - - + -
967 VAL* 4.0 19.5 - - + -
987 PRO* 5.3 2.7 - - + -
1017 HIS* 3.7 35.9 - - + +
1027 PRO 2.8 11.0 + - - +
1037 THR* 4.2 13.7 - - + +
1047 LEU* 2.9 23.8 + - - +
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Residues in contact with VAL 9 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87 LEU* 1.3 78.9 - - - +
107 CYS* 1.3 65.4 + - - +
117 ASP* 5.4 0.2 - - + -
197 ALA* 3.2 11.8 - - - -
207 GLY 3.0 11.0 + - - -
227 ALA* 4.2 16.2 - - + -
947 LEU* 6.4 0.4 - - - -
1047 LEU* 3.3 26.2 - - + +
1067 THR* 5.4 3.1 - - + -
3407 TRP* 2.8 59.0 + - + +
3437 GLY* 3.8 26.2 - - - +
3447 SER* 3.9 9.4 - - - +
3477 ALA* 4.5 1.1 - - + -
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Residues in contact with CYS 10 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87 LEU* 4.1 2.0 - - + -
97 VAL* 1.3 76.0 - - - +
117 ASP* 1.3 59.4 + - - +
127 ASN* 3.5 25.8 + - - -
177 VAL* 4.1 16.8 - - - -
187 LYS 3.6 2.7 - - - -
197 ALA* 4.5 4.7 - - + +
867 TRP* 4.0 17.7 - - - -
897 THR* 4.7 10.8 - - + -
907 PHE* 5.8 5.2 - - + -
1037 THR* 4.9 6.3 - - + -
1047 LEU 2.9 7.6 + - - +
1057 LEU* 3.5 19.6 - - + +
1067 THR* 3.4 22.9 + - - +
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Residues in contact with ASP 11 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97 VAL* 4.0 1.0 - - + -
107 CYS* 1.3 72.1 - - - +
127 ASN* 1.3 65.8 + - - +
137 GLY* 5.3 0.2 - - - -
177 VAL* 3.5 6.0 - - - -
187 LYS* 2.8 58.8 + - + +
1067 THR* 2.9 27.3 + - + +
1377 GLN* 4.2 7.3 - - - +
3397 VAL* 3.4 34.3 - - + +
3407 TRP* 4.0 16.9 + - + +
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Residues in contact with ASN 12 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107 CYS* 3.5 19.4 + - - -
117 ASP* 1.3 79.3 + - - +
137 GLY* 1.3 59.0 + - - +
167 LEU 4.7 0.2 - - - -
177 VAL* 4.6 9.5 - - + +
337 SER* 5.7 0.2 - - - -
717 ILE* 3.5 22.8 - - + +
747 GLY* 5.3 3.1 - - - +
767 ILE* 5.5 4.1 - - + +
827 MET* 3.5 11.9 - - + +
867 TRP* 2.9 38.4 + - - +
1057 LEU* 4.3 7.7 - - - +
1067 THR* 3.7 21.3 + - - +
1197 MET* 4.8 3.4 - - - +
1377 GLN* 4.1 15.1 + - - +
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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
------------------------------------------------------------
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