Contacts of the helix formed by residues 93 - 105 (chain K) 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 PRO 93 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20K ASP* 4.4 17.5 - - - +
23K GLU* 5.8 4.5 - - - +
91K ALA 4.1 4.7 - - - +
92K ASP* 1.3 98.4 - - - +
94K GLU* 1.3 67.4 + - - +
95K ASP* 4.4 9.2 - - + +
96K VAL* 3.0 29.6 + - + -
97K ILE* 3.1 11.0 - - - +
158K THR* 4.2 8.3 - - + +
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Residues in contact with GLU 94 (chain K).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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839J MLY 4.3 9.9 - - - -
93K PRO* 1.3 71.8 - - - +
95K ASP* 1.3 62.9 + - - +
97K ILE* 3.2 10.0 + - - +
98K MET* 2.9 43.2 + - - +
154K CYS* 3.4 15.5 - - + +
155K TYR* 3.2 41.4 - - + -
158K THR* 3.2 24.7 + - + +
159K HIS* 3.3 14.4 + - - -
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Residues in contact with ASP 95 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93K PRO* 3.1 6.5 + - + +
94K GLU* 1.3 82.5 + - - +
96K VAL* 1.3 63.6 + - + +
98K MET* 3.8 8.5 - - - +
99K GLY* 3.0 23.6 + - - -
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Residues in contact with VAL 96 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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815J CYS* 4.3 11.5 - - - -
92K ASP* 3.1 27.6 - - - +
93K PRO* 3.0 23.1 + - + +
95K ASP* 1.3 81.1 - - + +
97K ILE* 1.3 60.2 + - - +
99K GLY* 3.3 2.4 + - - +
100K ALA* 3.0 27.2 + - - +
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Residues in contact with ILE 97 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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815J CYS* 6.1 0.9 - - - -
816J ILE* 5.8 3.8 - - + -
819J ASN* 5.7 1.1 - - + -
92K ASP* 3.1 39.7 - - + +
93K PRO 3.1 11.6 + - - +
94K GLU* 3.6 4.3 - - - +
96K VAL* 1.3 78.2 - - - +
98K MET* 1.3 55.9 + - - +
100K ALA* 3.3 8.0 + - + +
101K PHE* 3.0 60.0 + - + -
154K CYS* 3.5 29.6 - - + +
157K ILE* 3.9 29.8 - - + -
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Residues in contact with MET 98 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94K GLU* 2.9 28.1 + - - +
95K ASP* 4.0 8.7 - - - +
97K ILE* 1.3 75.4 - - - +
99K GLY* 1.3 58.6 + - - +
101K PHE* 3.7 6.9 - - - +
102K LYS* 2.9 32.3 + - - +
150K TYR* 5.8 1.3 - - + -
151K LYS* 4.5 31.2 - - + -
154K CYS* 3.6 22.9 - - - -
155K TYR* 5.2 10.8 - - + -
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Residues in contact with GLY 99 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95K ASP 3.0 16.1 + - - -
96K VAL* 3.3 5.4 + - - -
97K ILE 3.3 0.4 - - - -
98K MET* 1.3 75.1 - - - +
100K ALA* 1.3 61.4 + - - +
102K LYS* 3.1 16.9 + - - +
103K VAL* 3.1 20.3 + - - +
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Residues in contact with ALA 100 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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812J SER* 4.9 17.9 - - - +
815J CYS* 5.8 4.9 - - + -
816J ILE* 3.9 29.8 - - + -
96K VAL 3.0 12.3 + - - +
97K ILE* 3.6 9.2 - - - +
99K GLY* 1.3 74.5 - - - +
101K PHE* 1.3 59.4 + - - +
103K VAL* 3.2 10.6 + - - +
104K LEU* 3.0 32.3 + - + +
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Residues in contact with PHE 101 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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816J ILE* 4.4 16.8 - - + -
97K ILE* 3.0 42.6 + - + +
98K MET* 3.7 6.1 - - - +
99K GLY 3.3 0.4 - - - -
100K ALA* 1.3 76.2 - - - +
102K LYS* 1.3 56.3 + - - +
104K LEU* 3.7 25.2 - - + +
105K ASP 2.9 21.3 + - - -
112K ILE* 5.7 0.2 - - + -
117K LEU* 5.2 13.9 - - + -
150K TYR* 3.1 52.3 + + + -
151K LYS 5.2 0.9 - - - -
153K ILE* 5.0 22.7 - - + -
154K CYS* 3.6 20.2 - - - -
157K ILE* 6.0 0.9 - - + -
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Residues in contact with LYS 102 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98K MET 2.9 18.5 + - - +
99K GLY* 3.1 7.6 + - - +
101K PHE* 1.3 75.2 - - - +
103K VAL* 1.3 62.4 + - + +
105K ASP* 3.0 28.8 - - - +
106K PRO* 3.2 9.1 - - + +
108K GLY* 3.6 28.1 - - - -
109K LYS* 3.7 11.5 - - - +
150K TYR* 4.9 4.7 - - + +
151K LYS* 5.4 8.6 - - - +
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Residues in contact with VAL 103 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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812J SER* 5.7 9.4 - - - +
99K GLY 3.1 17.6 + - - +
100K ALA* 3.4 9.9 - - - +
102K LYS* 1.3 80.2 - - + +
104K LEU* 1.3 64.1 + - + +
106K PRO* 3.7 17.9 - - - +
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Residues in contact with LEU 104 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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816J ILE* 4.6 10.8 - - + -
100K ALA* 3.0 13.1 + - + +
101K PHE* 3.7 38.6 - - + +
102K LYS 3.3 0.2 - - - -
103K VAL* 1.3 85.9 - - + +
105K ASP* 1.3 58.1 + - + +
106K PRO* 3.3 7.6 - - - +
112K ILE* 3.3 31.0 - - + +
116K PHE* 5.0 5.6 - - + -
117K LEU* 4.2 15.9 - - + -
120K LEU* 3.7 28.5 - - + -
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Residues in contact with ASP 105 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101K PHE 2.9 6.2 + - - +
102K LYS* 3.0 14.3 - - + +
104K LEU* 1.3 77.5 - - - +
106K PRO* 1.3 58.2 - - - +
107K ASP* 3.1 14.3 - - - +
108K GLY* 3.0 37.8 + - - +
109K LYS 3.8 0.7 + - - -
110K GLY* 2.9 28.6 + - - +
111K SER 4.9 0.7 - - - +
112K ILE* 4.8 10.2 + - + +
150K TYR* 2.9 25.1 + - + +
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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