Contacts of the helix formed by residues 97 - 111 (chain A) in PDB entry 1ML8
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 LYS 97 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A GLN* 3.3 15.3 - - - +
95A ASP 3.2 5.5 + - - +
96A LEU* 1.3 75.2 - - - +
98A ASP* 1.3 68.2 + - - +
99A ALA* 4.2 8.1 - - + +
100A ALA* 3.0 15.2 + - + +
101A VAL* 3.1 14.5 + - - +
131A VAL* 6.0 1.1 - - - -
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Residues in contact with ASP 98 (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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96A LEU 4.2 0.8 + - - -
97A LYS* 1.3 73.8 - - - +
99A ALA* 1.3 66.8 + - - +
101A VAL* 3.1 4.7 + - - +
102A ALA* 2.9 24.6 + - - +
129A TYR* 2.5 36.4 + - - -
131A VAL* 4.8 6.4 - - - +
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Residues in contact with ALA 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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97A LYS* 3.1 6.1 - - + +
98A ASP* 1.3 82.0 + - - +
100A ALA* 1.3 62.7 + - - +
102A ALA* 3.9 5.7 - - - +
103A ARG* 3.1 25.3 + - - +
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Residues in contact with ALA 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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55A ILE* 5.6 0.3 - - - +
56A LEU* 3.6 14.9 - - + +
61A GLN* 3.4 32.5 - - + +
97A LYS* 3.0 9.1 + - + +
99A ALA* 1.3 79.1 - - - +
101A VAL* 1.3 59.7 + - - +
103A ARG* 3.6 9.7 - - - +
104A ALA* 3.0 28.9 + - - +
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Residues in contact with VAL 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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56A LEU* 4.2 21.5 - - + -
91A VAL* 4.0 20.6 - - + -
96A LEU* 4.2 23.3 - - + -
97A LYS 3.1 11.3 + - - +
98A ASP 3.1 6.9 + - - +
100A ALA* 1.3 73.9 - - - +
102A ALA* 1.3 66.3 + - - +
104A ALA* 3.2 2.1 + - - +
105A VAL* 2.9 32.6 + - + +
129A TYR* 3.2 35.2 - - + -
131A VAL* 4.0 17.7 - - + -
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Residues in contact with ALA 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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98A ASP* 2.9 18.6 + - - +
99A ALA* 3.9 5.4 - - - +
101A VAL* 1.3 78.1 - - - +
103A ARG* 1.3 53.2 + - - +
105A VAL* 3.2 1.8 + - - +
106A ASP* 2.7 44.3 + - - +
129A TYR* 3.5 28.4 - - + +
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Residues in contact with ARG 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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55A ILE* 4.9 10.3 - - - +
99A ALA 3.1 18.5 + - - +
100A ALA* 3.6 8.7 - - - +
102A ALA* 1.3 74.4 - - - +
104A ALA* 1.3 58.6 + - - +
106A ASP* 3.0 6.6 + - - +
107A LEU* 2.9 64.1 + - + +
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Residues in contact with ALA 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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52A VAL* 3.6 13.7 - - + +
55A ILE* 3.8 33.7 - - + +
56A LEU* 3.9 21.3 - - + -
100A ALA 3.0 18.6 + - - +
101A VAL 3.7 3.4 - - - +
103A ARG* 1.3 76.0 - - - +
105A VAL* 1.3 59.5 + - - +
107A LEU* 4.4 1.0 - - - +
108A SER* 3.0 30.3 + - - -
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Residues in contact with VAL 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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52A VAL* 3.9 17.9 - - + -
89A PHE* 3.6 35.2 - - + -
91A VAL* 5.1 0.2 - - + -
101A VAL* 2.9 28.3 + - + +
102A ALA 3.8 2.9 - - - +
104A ALA* 1.3 75.1 - - - +
106A ASP* 1.3 63.9 + - - +
108A SER* 3.7 0.7 - - - -
109A ALA* 3.0 24.6 + - - +
127A HIS* 3.6 25.6 - - + -
128A SER 4.6 0.9 - - - +
129A TYR* 3.9 33.0 - - + -
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Residues in contact with ASP 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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102A ALA* 2.7 23.1 + - - +
103A ARG* 3.4 7.0 - - - +
105A VAL* 1.3 78.4 - - - +
107A LEU* 1.3 61.0 + - + +
109A ALA* 3.9 0.3 - - - -
110A GLU* 3.0 53.2 + - - +
127A HIS* 3.5 22.1 + - - -
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Residues in contact with LEU 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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55A ILE* 4.7 16.2 - - + -
103A ARG* 2.9 63.4 + - + +
104A ALA* 4.4 2.0 - - - +
106A ASP* 1.3 74.1 - - + +
108A SER* 1.3 60.9 + - - +
111A LYS* 2.8 36.4 + - + +
112A TYR* 2.8 46.4 + - + +
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Residues in contact with SER 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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48A SER* 3.0 32.4 + - - -
51A ASP* 3.4 22.4 + - - +
52A VAL* 3.6 15.2 - - - +
55A ILE* 5.5 1.9 - - - +
89A PHE* 5.6 0.4 - - - -
104A ALA 3.0 21.4 + - - -
105A VAL 3.7 1.3 - - - -
107A LEU* 1.3 79.5 - - - +
109A ALA* 1.3 60.7 + - - +
112A TYR* 4.4 2.5 - - - -
113A CYS* 3.0 31.7 + - - +
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Residues in contact with ALA 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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48A SER* 4.5 11.2 - - - +
87A LEU* 4.9 8.1 - - + -
89A PHE* 5.4 2.5 - - + -
105A VAL* 3.0 18.5 + - + +
108A SER* 1.3 77.5 - - - +
110A GLU* 1.3 61.3 + - + +
113A CYS* 5.2 0.2 - - - -
116A ALA* 3.7 17.9 - - + +
117A LEU* 4.7 1.8 - - - +
120A GLU* 3.7 14.6 - - - +
125A ILE* 5.8 4.5 - - + +
127A HIS* 3.5 35.4 - - + +
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Residues in contact with GLU 110 (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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106A ASP* 3.0 28.7 + - - +
109A ALA* 1.3 81.0 - - + +
111A LYS* 1.3 61.7 + - + +
117A LEU* 3.5 19.2 - - - +
120A GLU* 4.3 19.3 - - - +
127A HIS* 2.6 36.1 + - + -
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Residues in contact with LYS 111 (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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107A LEU* 2.8 30.8 + - + +
109A ALA 3.8 0.2 - - - -
110A GLU* 1.3 82.5 - - + +
112A TYR* 1.3 94.8 + - + +
117A LEU* 3.5 17.0 - - - +
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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