Contacts of the helix formed by residues 98 - 109 (chain J) 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 HIS 98 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39J PHE* 4.4 0.9 - + - -
78J PHE* 3.1 41.4 - + + +
79J SER* 2.8 36.9 + - - -
80J MET* 4.8 0.7 - - - -
96J HIS* 3.3 28.3 + + + -
97J LEU* 1.3 76.9 - - - +
99J GLU* 1.3 67.7 + - - +
100J PRO* 3.2 12.6 - - + -
101J ALA* 3.2 26.2 + - + +
102J VAL* 3.5 19.9 - - - +
701J LEU* 5.2 1.5 - - - +
704J ILE* 4.8 5.9 - - - +
708J ARG* 4.3 7.6 - - - +
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Residues in contact with GLU 99 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47J PHE* 3.9 20.8 - - + -
78J PHE* 5.6 3.7 - - + -
98J HIS* 1.3 75.0 - - - +
100J PRO* 1.3 73.1 - - + +
102J VAL* 3.2 13.8 + - - +
103J LEU* 3.3 12.4 + - - +
692J LEU* 4.2 10.7 - - + +
695J LEU* 5.4 0.5 - - - +
696J ARG* 2.3 44.7 + - - -
701J LEU* 3.6 28.5 - - + +
705J ARG* 4.2 19.9 + - - -
708J ARG* 5.2 0.4 - - - +
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Residues in contact with PRO 100 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39J PHE* 3.7 26.9 - - + -
47J PHE* 3.5 45.3 - - + -
78J PHE* 3.8 20.6 - - + -
98J HIS* 3.2 12.3 - - + -
99J GLU* 1.3 91.6 - - + +
101J ALA* 1.3 64.0 + - - +
102J VAL 2.9 2.8 + - - -
103J LEU* 3.0 6.4 + - + +
104J TYR* 2.8 29.5 + - + +
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Residues in contact with ALA 101 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39J PHE* 3.9 15.1 - - + -
81J ASN* 3.5 10.3 - - - +
94J MET* 3.0 36.3 - - + +
96J HIS 3.6 3.8 - - - +
98J HIS* 3.2 29.1 + - + +
99J GLU 3.4 0.8 - - - -
100J PRO* 1.3 78.5 - - - +
102J VAL* 1.3 56.9 + - - +
104J TYR* 3.9 1.4 - - - +
105J ASN* 3.1 22.5 + - - +
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Residues in contact with VAL 102 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91J MET* 3.9 30.3 - - + +
94J MET* 4.8 5.8 - - + -
96J HIS 5.7 0.2 - - - +
97J LEU* 5.7 2.7 - - + -
98J HIS 3.5 17.4 + - - +
99J GLU 3.2 8.0 + - - +
100J PRO 2.9 1.2 - - - -
101J ALA* 1.3 76.7 - - + +
103J LEU* 1.3 71.6 + - - +
105J ASN 3.4 0.2 + - - -
106J LEU* 3.3 24.5 + - + +
119J SER* 5.4 0.7 - - - +
695J LEU* 3.8 22.2 - - + -
700J VAL* 4.6 8.3 - - + -
701J LEU* 4.4 11.4 - - + -
704J ILE* 4.3 23.1 - - + -
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Residues in contact with LEU 103 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46J SER* 5.0 0.7 - - - -
47J PHE* 4.8 6.7 - - + -
99J GLU 3.3 8.8 + - - +
100J PRO* 3.0 8.7 + - + +
102J VAL* 1.3 84.9 - - - +
104J TYR* 1.3 79.0 + - + +
106J LEU* 3.1 3.3 + - - +
107J MLY 3.0 19.8 + - + +
686J MET* 3.5 22.9 - - + -
688J HIS* 4.0 33.2 - - + +
691J VAL* 4.5 16.2 - - + -
692J LEU* 3.6 39.3 - - + -
695J LEU* 4.7 6.2 - - + +
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Residues in contact with TYR 104 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39J PHE* 3.5 37.2 - + + -
47J PHE* 2.5 38.5 + - + -
48J VAL* 3.1 20.0 - - - +
49J MLY 4.3 23.6 - - + -
100J PRO* 2.8 23.2 + - + +
101J ALA* 4.3 1.8 - - - +
103J LEU* 1.3 88.2 - - + +
105J ASN* 1.3 55.3 + - - +
107J MLY 3.7 33.1 - - + +
108J GLU* 3.0 43.1 + - + +
688J HIS* 3.6 19.7 - + - -
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Residues in contact with ASN 105 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85J TYR 4.5 2.8 - - - +
86J ASP 2.9 28.5 - - - +
87J MLY 3.5 1.3 - - - -
88J ILE* 3.1 39.5 + - - +
91J MET* 3.4 28.3 - - + +
94J MET* 4.8 8.1 - - + +
101J ALA 3.1 18.7 + - - +
102J VAL 3.4 0.2 + - - -
103J LEU 3.3 0.2 - - - -
104J TYR* 1.3 73.2 - - - +
106J LEU* 1.3 68.0 + - - +
108J GLU* 4.1 3.2 - - - +
109J ARG* 2.9 38.3 + - - +
117J THR* 4.0 1.2 + - - -
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Residues in contact with LEU 106 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91J MET* 3.1 32.8 - - + -
102J VAL* 3.3 24.2 + - + +
103J LEU* 3.1 7.8 + - - +
105J ASN* 1.3 83.1 - - - +
107J MLY 1.3 65.0 + - - +
109J ARG* 3.0 14.0 + - - +
110J TYR* 3.2 14.0 + - - +
114J MET 5.0 0.9 - - - +
117J THR* 3.4 26.2 - - + +
124J VAL* 4.4 17.7 - - + -
126J VAL* 5.1 10.6 - - + +
675J ILE* 5.4 1.6 - - + -
686J MET* 4.1 9.6 - - + -
691J VAL* 4.6 9.0 - - + -
695J LEU* 4.4 22.0 - - + -
700J VAL* 6.1 0.9 - - + -
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Residues in contact with MLY 107 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45J GLN* 4.9 8.3 - - - -
103J LEU* 3.0 9.2 + - + +
104J TYR* 3.7 32.8 - - + +
106J LEU* 1.3 80.0 + - - +
108J GLU* 1.3 66.5 + - + +
110J TYR* 3.2 6.7 + - + +
111J ALA* 3.1 23.8 + - + +
686J MET* 3.0 46.6 - - + +
688J HIS* 2.9 41.5 + - + +
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Residues in contact with GLU 108 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49J MLY 2.8 47.9 - - - -
86J ASP* 3.7 29.5 - - - +
87J MLY 4.2 19.9 - - + -
104J TYR* 3.0 30.5 + - + +
105J ASN* 3.5 3.7 + - - +
106J LEU 3.3 0.2 - - - -
107J MLY 1.3 81.7 + - + +
109J ARG* 1.3 57.9 + - - +
110J TYR 3.0 3.9 + - - -
111J ALA* 3.4 15.1 + - - +
112J ALA* 3.5 12.1 + - - +
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Residues in contact with ARG 109 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17J LEU 4.2 8.1 + - - -
18J ARG* 6.0 0.6 - - - +
87J MLY 2.9 46.4 + - + +
88J ILE 3.9 3.8 + - - -
89J GLU* 3.7 20.4 + - - +
105J ASN* 2.9 32.3 + - - +
106J LEU 3.0 4.6 + - - +
108J GLU* 1.3 74.5 - - - +
110J TYR* 1.3 51.1 + - - +
112J ALA* 3.9 4.7 - - - -
114J MET* 2.4 84.1 + - - +
116J TYR 2.8 29.9 + - - -
117J THR* 3.4 31.7 - - + +
153J PRO* 4.2 2.8 - - - +
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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