Contacts of the helix formed by residues 98 - 109 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A PHE* 4.4 1.1 - + - -
78A PHE* 3.1 41.6 - + + +
79A SER* 2.8 36.2 + - - -
80A MET* 4.8 0.7 - - - -
96A HIS* 3.3 29.4 + + + -
97A LEU* 1.3 77.1 - - - +
99A GLU* 1.3 68.0 + - - +
100A PRO* 3.2 12.8 - - + -
101A ALA* 3.2 27.0 + - + +
102A VAL* 3.5 20.1 + - - +
701A LEU* 5.2 1.5 - - - +
704A ILE* 4.8 5.4 - - - +
708A ARG* 4.3 7.4 - - - +
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Residues in contact with GLU 99 (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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47A PHE* 3.9 20.9 - - + -
78A PHE* 5.6 3.0 - - + -
98A HIS* 1.3 75.7 - - - +
100A PRO* 1.3 72.3 - - + +
102A VAL* 3.2 13.6 + - - +
103A LEU* 3.3 12.6 + - - +
692A LEU* 4.2 9.9 - - + +
695A LEU* 5.4 0.5 - - - +
696A ARG* 2.3 44.2 + - - -
701A LEU* 3.6 28.8 - - + +
705A ARG* 4.2 19.6 + - - -
708A ARG* 5.2 0.8 - - - +
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Residues in contact with PRO 100 (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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39A PHE* 3.7 27.4 - - + -
47A PHE* 3.6 46.4 - - + -
78A PHE* 3.8 20.2 - - + -
98A HIS* 3.2 12.1 - - + -
99A GLU* 1.3 91.8 - - + +
101A ALA* 1.3 65.5 + - - +
102A VAL 2.9 2.1 + - - -
103A LEU* 3.0 6.2 + - + +
104A TYR* 2.8 27.9 + - + +
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Residues in contact with ALA 101 (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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39A PHE* 3.9 15.4 - - + -
81A ASN* 3.5 9.9 - - - +
94A MET* 3.0 36.1 - - + +
96A HIS 3.6 3.8 - - - +
98A HIS* 3.2 29.0 + - + +
99A GLU 3.4 0.6 - - - -
100A PRO* 1.3 78.8 - - - +
102A VAL* 1.3 56.5 + - - +
104A TYR* 3.9 0.8 - - - +
105A ASN* 3.1 22.9 + - - +
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Residues in contact with VAL 102 (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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91A MET* 3.9 31.0 - - + +
94A MET* 4.9 5.8 - - + -
96A HIS 5.7 0.2 - - - +
97A LEU* 5.7 2.9 - - + -
98A HIS 3.5 16.6 + - - +
99A GLU 3.2 8.6 + - - +
100A PRO 2.9 1.2 - - - -
101A ALA* 1.3 77.1 - - - +
103A LEU* 1.3 69.7 + - - +
105A ASN 3.4 0.3 + - - -
106A LEU* 3.3 23.7 + - + +
119A SER* 5.4 0.7 - - - +
695A LEU* 3.8 22.4 - - + -
700A VAL* 4.6 8.5 - - + -
701A LEU* 4.4 11.9 - - + -
704A ILE* 4.3 22.4 - - + -
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Residues in contact with LEU 103 (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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46A SER* 5.0 0.4 - - - -
47A PHE* 4.8 7.4 - - + -
99A GLU 3.3 9.2 + - - +
100A PRO* 3.0 8.2 + - + +
102A VAL* 1.3 84.4 - - - +
104A TYR* 1.3 77.9 + - + +
106A LEU* 3.1 3.1 + - - +
107A MLY 3.0 20.2 + - + +
686A MET* 3.5 23.1 - - + -
688A HIS* 4.0 33.4 - - + +
691A VAL* 4.5 16.6 - - + -
692A LEU* 3.6 38.4 - - + +
695A LEU* 4.7 5.1 - - + +
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Residues in contact with TYR 104 (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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39A PHE* 3.5 36.8 - + + -
47A PHE* 2.5 40.1 + - + -
48A VAL* 3.1 20.5 - - - +
49A MLY 4.3 23.6 - - + -
100A PRO* 2.8 24.4 + - + +
101A ALA 4.3 1.6 - - - +
103A LEU* 1.3 87.3 - - + +
105A ASN* 1.3 55.4 + - - +
107A MLY 3.7 32.7 - - + +
108A GLU* 3.1 42.7 + - + +
688A HIS* 3.6 18.5 - + - -
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Residues in contact with ASN 105 (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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85A TYR 4.5 2.1 - - - +
86A ASP 2.9 28.1 - - - +
87A MLY 3.5 1.1 - - - -
88A ILE* 3.1 38.7 + - - +
91A MET* 3.4 27.8 - - + +
94A MET* 4.8 8.3 - - + +
101A ALA 3.1 19.1 + - - +
103A LEU 3.3 0.6 - - - -
104A TYR* 1.3 72.8 - - - +
106A LEU* 1.3 67.3 + - - +
108A GLU* 3.5 3.0 + - - +
109A ARG* 2.9 37.8 + - - +
117A THR* 4.0 1.2 + - - -
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Residues in contact with LEU 106 (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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91A MET* 3.1 33.2 - - + -
102A VAL* 3.3 24.4 + - + +
103A LEU* 3.3 7.4 - - - +
105A ASN* 1.3 82.6 - - - +
107A MLY 1.3 64.7 + - - +
109A ARG* 3.0 12.6 + - - +
110A TYR* 3.2 14.3 + - - +
114A MET 5.0 0.9 - - - +
117A THR* 3.4 27.2 - - + +
124A VAL* 4.4 18.6 - - + -
126A VAL* 5.1 9.3 - - + +
675A ILE* 5.4 1.6 - - + -
686A MET* 4.1 9.4 - - + -
691A VAL* 4.6 9.4 - - + -
695A LEU* 4.4 22.0 - - + -
700A VAL* 6.2 1.1 - - + -
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Residues in contact with MLY 107 (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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45A GLN* 4.9 9.4 - - - -
103A LEU* 3.0 9.3 + - + +
104A TYR* 3.7 32.1 - - + +
106A LEU* 1.3 79.9 + - - +
108A GLU* 1.3 66.1 + - + +
110A TYR* 3.2 5.7 + - + +
111A ALA* 3.1 24.2 + - + +
686A MET* 3.0 48.6 - - + +
688A HIS* 2.9 42.2 + - + +
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Residues in contact with GLU 108 (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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49A MLY 2.8 47.4 - - - -
86A ASP* 3.7 29.9 - - - +
87A MLY 4.2 20.5 - - + -
104A TYR* 3.1 29.9 + - + +
105A ASN* 4.3 3.0 - - - +
106A LEU 3.3 0.4 - - - -
107A MLY 1.3 81.4 + - + +
109A ARG* 1.3 59.0 + - - +
110A TYR 3.1 4.0 + - - -
111A ALA* 3.4 13.8 + - - +
112A ALA* 3.5 12.1 + - - +
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Residues in contact with ARG 109 (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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17A LEU 4.2 8.5 + - - -
18A ARG* 6.0 1.0 - - - +
87A MLY 2.9 46.2 + - + +
88A ILE 3.9 3.6 + - - -
89A GLU* 3.7 19.4 + - - +
105A ASN* 2.9 32.7 + - - +
106A LEU 3.0 4.4 + - - +
108A GLU* 1.3 74.9 - - - +
110A TYR* 1.3 50.9 + - - +
112A ALA* 3.9 4.5 - - - -
114A MET* 2.4 84.3 + - - +
116A TYR 2.8 29.7 + - - -
117A THR* 3.4 31.5 - - + +
153A PRO* 4.2 3.0 - - - +
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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