Contacts of the strand formed by residues 52 - 59 (chain A) in PDB entry 4LGD
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 VAL 52 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A LYS* 4.4 13.7 - - - -
44A ALA 3.4 15.9 - - - +
45A ILE* 4.5 10.1 - - + +
50A GLY 4.2 8.3 - - - +
51A GLN* 1.3 79.9 - - - +
53A VAL* 1.3 67.2 + - - +
86A TYR* 5.7 0.9 - - - -
101A TYR* 3.4 52.1 + - + +
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Residues in contact with VAL 53 (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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27A PHE* 3.7 37.9 - - + -
44A ALA* 2.9 43.0 + - + +
45A ILE 4.7 0.2 - - - +
46A HIS* 4.6 2.2 - - + -
51A GLN* 3.4 16.1 + - + +
52A VAL* 1.3 79.9 - - - +
54A ALA* 1.3 62.0 + - - +
55A ILE* 4.4 1.8 - - + -
86A TYR* 4.5 16.6 - - + -
98A VAL* 3.9 17.9 - - + -
99A MET 3.8 10.8 - - - +
101A TYR* 3.8 15.5 - - - +
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Residues in contact with ALA 54 (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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33A LEU* 5.6 1.1 - - + -
41A VAL* 5.1 9.4 - - + -
42A PHE 3.5 10.1 - - - +
44A ALA 4.7 0.2 - - - +
53A VAL* 1.3 72.8 - - - +
55A ILE* 1.3 72.2 + - - +
97A ILE 4.2 0.2 - - - -
98A VAL* 3.3 3.8 - - - +
99A MET* 2.9 49.4 + - + +
100A GLU 4.1 12.8 - - - +
101A TYR* 4.2 11.6 - - + +
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Residues in contact with ILE 55 (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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27A PHE* 3.9 28.9 - - + -
29A VAL* 4.1 13.2 - - + -
40A SER 4.0 0.9 - - - +
41A VAL* 3.9 1.7 - - - -
42A PHE* 3.0 46.6 + - + +
44A ALA* 3.6 26.5 - - + -
53A VAL* 4.4 2.2 - - + -
54A ALA* 1.3 81.8 - - - +
56A LYS* 1.3 70.4 + - - +
57A GLN* 4.6 6.5 - - + +
96A TRP* 3.8 36.1 - - + -
97A ILE 3.3 5.8 - - - +
98A VAL* 4.3 13.5 - - + -
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Residues in contact with LYS 56 (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 GLY 6.3 0.4 - - - +
38A TYR* 4.3 30.5 - - - +
39A GLY 4.7 5.6 - - - -
40A SER 3.5 11.4 - - - +
41A VAL* 4.0 23.3 - - + +
54A ALA 4.3 0.2 - - - -
55A ILE* 1.3 75.1 - - - +
57A GLN* 1.3 66.8 + - - +
58A VAL* 4.2 22.1 - - + +
67A ILE* 5.7 3.4 - - - +
70A GLU* 5.8 2.0 + - - -
95A LEU 3.5 3.9 - - - +
96A TRP* 3.6 3.8 - - - -
97A ILE* 3.0 49.4 + - + +
99A MET* 5.9 10.9 - - + +
164A ASP* 5.5 4.9 + - - -
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Residues in contact with GLN 57 (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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29A VAL* 5.5 5.3 - - - +
39A GLY* 3.3 23.0 - - - -
40A SER* 3.0 15.5 + - - +
42A PHE* 3.5 30.2 - - - -
55A ILE* 4.6 8.2 - - + +
56A LYS* 1.3 78.7 - - - +
58A VAL* 1.3 63.3 + - - +
59A PRO* 4.3 1.2 - - - +
94A ASP* 4.7 16.8 - - + +
95A LEU 3.9 3.4 - - - -
96A TRP* 3.4 47.2 - - + +
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Residues in contact with VAL 58 (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 TYR* 3.3 19.3 - - + +
56A LYS* 4.3 22.7 - - + +
57A GLN* 1.3 76.2 - - - +
59A PRO* 1.3 70.2 - - + +
60A VAL* 5.0 1.3 - - - +
62A SER* 5.9 0.2 - - - +
67A ILE* 4.4 32.1 - - + -
94A ASP* 3.3 7.8 - - - -
95A LEU* 2.9 60.3 + - + +
97A ILE* 4.6 9.0 - - + -
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Residues in contact with PRO 59 (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 TYR 3.6 15.3 - - - +
39A GLY* 4.9 2.2 - - - -
57A GLN 4.3 2.7 - - - +
58A VAL* 1.3 85.8 - - + +
60A VAL* 1.3 66.1 + - - +
61A GLU* 3.1 23.0 + - + +
62A SER* 2.9 40.4 + - - +
93A THR* 3.7 8.3 - - - +
94A ASP* 3.9 6.9 - - - +
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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