Contacts of the strand formed by residues 16 - 21 (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 16 (chain 7).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137 GLY* 3.1 16.8 + - - -
157 GLY* 1.3 82.4 - - - +
177 VAL* 1.3 59.2 + - - +
187 LYS* 2.7 39.0 + - + +
307 VAL* 3.8 16.4 - - + -
317 PHE* 3.5 30.1 - - - +
327 PRO* 3.8 9.0 - - + -
337 SER* 4.6 1.8 - - - -
1577 ASP* 5.2 5.6 - - + +
2107 ARG* 6.1 2.5 - - - +
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Residues in contact with VAL 17 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107 CYS* 4.1 24.2 - - - -
117 ASP 3.5 11.0 - - - +
127 ASN* 4.6 8.3 - - - +
137 GLY 4.6 0.4 - - - +
167 LEU* 1.3 74.5 - - - +
187 LYS* 1.3 69.2 + - - +
297 ALA 3.6 0.6 - - - +
307 VAL* 3.2 24.3 - - - +
317 PHE* 3.0 38.7 + - + +
337 SER* 4.0 13.5 - - - +
827 MET* 5.8 0.9 - - + -
857 ILE* 3.7 28.5 - - + -
867 TRP* 6.1 0.2 - - + -
897 THR* 4.5 7.6 - - + +
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Residues in contact with LYS 18 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107 CYS* 3.6 0.5 - - - -
117 ASP* 2.8 60.0 + - + +
137 GLY* 4.3 8.7 - - - -
167 LEU* 2.7 39.8 + - + +
177 VAL* 1.3 77.8 - - - +
197 ALA* 1.3 62.3 + - - +
277 PRO* 4.0 7.4 - - + -
297 ALA 3.3 4.3 - - - -
307 VAL* 4.2 7.4 - - + -
3367 LYS 5.1 4.5 - - - +
3377 TYR* 3.8 33.7 - - + -
3407 TRP* 3.4 20.8 - - + -
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Residues in contact with ALA 19 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97 VAL 3.2 11.4 - - - +
107 CYS* 4.6 5.6 - - + -
177 VAL* 4.7 2.9 - - + -
187 LYS* 1.3 76.2 - - - +
207 GLY* 1.3 52.4 + - - +
277 PRO* 3.2 4.2 - - - +
287 ARG 2.6 30.8 + - - -
297 ALA* 2.7 27.3 + - + +
897 THR* 3.6 31.6 - - + -
947 LEU* 4.0 6.5 - - + -
3407 TRP* 3.6 4.5 - - - +
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Residues in contact with GLY 20 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87 LEU* 3.6 6.9 - - - +
97 VAL 3.0 25.1 + - - -
197 ALA* 1.3 79.4 - - - +
217 PHE* 1.3 66.5 + - - -
287 ARG* 3.7 18.8 - - - -
947 LEU* 3.6 13.0 - - - +
3407 TRP* 3.6 10.8 - - - -
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Residues in contact with PHE 21 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57 THR 3.8 22.9 - - - +
77 ALA 3.5 2.2 - - - -
87 LEU* 3.5 28.7 - - + -
207 GLY* 1.3 75.0 - - - -
227 ALA* 1.3 67.4 + - - +
247 ASP* 3.0 34.9 + - - +
287 ARG* 3.5 37.5 - - + +
947 LEU* 4.3 27.1 - - + -
967 VAL* 3.7 26.9 - - + -
1017 HIS* 4.6 7.0 - + - -
3407 TRP* 3.5 9.4 - - - -
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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