Contacts of the strand formed by residues 73 - 79 (chain A) in PDB entry 2LMC
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 GLU 73 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A VAL* 3.7 2.2 - - - -
41A GLU* 2.8 51.7 + - + +
68A VAL* 5.2 2.9 - - + -
71A GLY 3.8 3.1 + - - +
72A PHE* 1.3 71.2 - - - +
74A VAL* 1.3 71.1 + - - +
40B THR* 5.3 5.6 - - + -
41B LYS* 2.8 54.0 + - + +
43B LYS* 4.8 5.8 + - - +
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Residues in contact with VAL 74 (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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38A ALA* 5.4 4.9 - - + -
39A THR 3.9 7.0 - - - +
40A VAL* 3.9 9.2 - - + -
63A ALA* 3.2 31.9 - - + +
64A GLU* 4.1 5.4 - - - +
67A TYR* 4.3 13.5 - - + -
68A VAL* 5.0 3.2 - - + +
72A PHE 3.8 1.0 + - - -
73A GLU* 1.3 80.7 - - - +
75A THR* 1.3 52.8 + - - +
76A ARG* 4.9 2.5 - - - +
77A VAL* 5.4 2.0 - - + -
40B THR* 4.3 19.3 - - + -
43B LYS* 2.7 36.2 + - - -
60B MET* 3.7 31.6 - - + -
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Residues in contact with THR 75 (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 THR* 2.7 27.1 + - + -
40A VAL 3.9 0.9 - - - -
41A GLU* 3.2 41.5 + - - +
74A VAL* 1.3 74.4 - - - +
76A ARG* 1.3 61.3 + - + +
43B LYS* 3.0 22.3 - - - +
62B PRO* 3.4 1.7 - - - +
64B TRP* 3.0 31.9 - - + -
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Residues in contact with ARG 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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39A THR* 2.8 40.8 + - + +
74A VAL* 3.9 1.4 - - - +
75A THR* 1.3 84.9 - - + +
77A VAL* 1.3 74.9 + - - +
78A ARG* 3.9 33.4 - - - +
43B LYS* 5.0 1.3 - - - +
60B MET* 4.6 2.5 - - - -
62B PRO* 3.4 31.6 - - + -
64B TRP* 5.1 5.4 - - + -
65B ARG* 5.1 19.0 - - - +
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Residues in contact with VAL 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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37A TRP 3.1 14.1 - - - +
38A ALA* 3.7 19.5 - - + -
51A ILE* 6.2 0.2 - - + -
60A LEU* 5.7 0.2 - - + -
63A ALA* 4.4 5.6 - - + -
74A VAL* 5.4 1.8 - - + -
76A ARG* 1.3 87.5 + - - +
78A ARG* 1.3 68.0 + - - +
79A PRO* 4.4 4.3 - - + -
59B GLU* 4.1 16.7 - - + +
60B MET* 3.2 70.0 + - + +
61B ILE* 5.7 0.5 - - - +
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Residues in contact with ARG 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A TRP* 2.7 43.3 + - + +
76A ARG* 3.9 33.0 - - - +
77A VAL* 1.3 83.4 - - - +
79A PRO* 1.3 75.6 + - - +
80A CYS* 3.5 1.4 + - - +
24B PRO* 4.2 27.0 - - - +
59B GLU* 5.4 2.2 - - - +
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Residues in contact with PRO 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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36A PHE* 3.9 28.9 - - + -
56A LEU* 3.9 11.4 - - + -
77A VAL* 4.2 4.5 - - + -
78A ARG* 1.3 95.5 + - + +
80A CYS* 1.3 60.5 + - - +
81A VAL* 3.8 4.4 + - + +
57B TYR* 4.5 18.4 + - + +
58B GLU 3.9 8.7 - - - +
59B GLU* 3.5 43.3 - - + +
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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