Contacts of the helix formed by residues 75 - 84 (chain A) in PDB entry 1LTM
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 ARG 75 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A MET* 3.6 35.8 + - - +
61A GLN* 3.0 42.4 + - - +
64A ILE* 3.8 16.6 - - + +
65A ASP* 2.9 29.1 + - - -
68A VAL* 3.5 25.0 - - + +
73A PHE 3.8 0.2 + - - -
74A ASP* 1.3 75.0 + - - +
76A GLN* 1.3 69.7 + - - +
78A LEU* 3.4 1.7 + - - +
79A GLN* 2.7 74.7 + - + +
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Residues in contact with GLN 76 (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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42A GLU 6.0 0.7 - - - +
43A PRO 4.0 13.4 - - - +
44A GLN* 3.4 36.8 + - + +
45A HIS* 4.0 12.8 + - - +
47A VAL* 2.9 30.8 + - + +
48A MET* 4.2 3.2 - - - -
74A ASP* 3.3 16.1 + - - +
75A ARG* 1.3 96.2 - - - +
77A GLN* 1.3 66.6 + - + +
79A GLN* 3.3 9.6 + - - +
80A GLU* 3.1 32.6 + - - +
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Residues in contact with GLN 77 (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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73A PHE* 6.6 0.2 - - + -
74A ASP* 3.1 39.7 + - + +
76A GLN* 1.3 77.4 - - + +
78A LEU* 1.3 63.2 + - - +
80A GLU* 3.2 14.1 + - - +
81A ILE* 3.2 29.8 + - + +
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Residues in contact with LEU 78 (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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63A PHE* 4.7 2.0 - - + -
64A ILE* 3.9 33.2 - - + +
67A MET* 3.5 35.4 - - + -
68A VAL* 5.1 0.4 - - + -
73A PHE* 4.3 21.3 - - + -
74A ASP 2.9 15.3 + - - +
75A ARG 3.8 3.1 - - - +
77A GLN* 1.3 78.3 - - - +
79A GLN* 1.3 56.3 + - - +
81A ILE* 3.2 18.2 + - + +
82A LEU* 2.9 41.7 + - + +
200A LEU* 3.8 26.0 - - + -
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Residues in contact with GLN 79 (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 VAL* 3.0 29.9 + - - +
48A MET 3.3 18.1 - - - +
49A GLN* 4.5 1.3 - - - +
50A MET* 3.7 31.0 + - + +
61A GLN* 5.1 1.0 + - - -
64A ILE* 4.1 12.1 - - + +
75A ARG* 2.7 63.5 + - + +
76A GLN* 3.3 15.9 + - - +
78A LEU* 1.3 75.9 - - - +
80A GLU* 1.3 58.7 + - + +
82A LEU* 4.7 0.4 - - - -
83A SER* 2.8 32.4 + - - -
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Residues in contact with GLU 80 (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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44A GLN* 4.7 11.6 - - - +
76A GLN* 3.1 21.4 + - - +
77A GLN* 3.5 14.4 - - - +
78A LEU 3.2 0.2 - - - -
79A GLN* 1.3 73.6 - - + +
81A ILE* 1.3 64.9 + - + +
83A SER* 2.8 20.6 + - - +
84A GLN* 3.0 21.7 + - - +
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Residues in contact with ILE 81 (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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73A PHE* 6.0 4.0 - - + -
77A GLN* 3.2 20.1 + - + +
78A LEU* 3.2 18.1 + - + +
80A GLU* 1.3 78.3 - - + +
82A LEU* 1.3 62.3 + - + +
84A GLN* 3.0 32.5 + - - +
85A ALA 3.5 4.0 + - - -
175A LEU* 3.7 32.9 - - + +
200A LEU* 4.9 7.0 - - + -
210A PRO* 4.1 28.5 - - + -
211A LEU* 4.3 6.9 - - + +
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Residues in contact with LEU 82 (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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50A MET* 3.9 21.1 - - + +
51A GLY 4.7 0.3 - - - +
52A GLY* 5.5 0.2 - - - -
54A PHE* 4.2 9.8 + - + +
60A ALA 4.7 1.3 - - - +
63A PHE* 4.3 15.5 - - + -
64A ILE* 3.8 31.6 - - + -
78A LEU* 2.9 30.6 + - + +
81A ILE* 1.3 73.0 - - + +
83A SER* 1.3 60.9 + - - +
84A GLN 3.0 5.8 - - - -
85A ALA* 3.1 28.2 + - + +
175A LEU* 4.2 24.5 - - + -
179A ALA* 4.7 2.9 - - + -
183A PHE* 4.4 24.9 - - + -
196A LEU* 4.9 5.6 - - + -
200A LEU* 5.4 0.9 - - + -
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Residues in contact with SER 83 (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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50A MET* 4.1 4.2 - - - -
51A GLY* 3.4 35.2 - - - -
52A GLY* 3.5 19.2 - - - -
79A GLN 2.8 17.6 + - - -
80A GLU* 2.8 24.3 + - - +
82A LEU* 1.3 76.7 - - - +
84A GLN* 1.3 62.3 + - - +
85A ALA 3.4 1.6 - - - +
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Residues in contact with GLN 84 (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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80A GLU* 3.0 26.7 + - - +
81A ILE* 3.0 10.1 + - - +
82A LEU 3.0 0.4 - - - -
83A SER* 1.3 83.7 - - - +
85A ALA* 1.3 60.6 + - - +
86A LYS* 3.7 5.0 + - - +
173A ARG* 2.8 25.8 + - - +
211A LEU* 3.3 37.8 - - + +
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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