Contacts of the strand formed by residues 57 - 64 (chain A) in PDB entry 5LEK
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 ILE 57 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A LYS* 5.5 3.6 - - - +
49A THR* 4.7 9.0 - - + -
50A SER 3.6 5.8 - - - +
51A ILE* 4.2 19.7 - - + -
55A GLY 3.8 12.3 - - - +
56A THR* 1.3 76.9 - - - +
58A MET* 1.3 67.4 + - - +
59A ASN* 3.8 19.1 - - - +
176A TYR* 3.6 59.0 - - + +
136B ILE* 5.9 1.8 - - - +
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Residues in contact with MET 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A THR* 3.1 8.8 - - - -
50A SER* 2.9 45.2 + - - +
56A THR 5.4 0.2 - - - +
57A ILE* 1.3 76.4 - - - +
59A ASN* 1.3 76.3 + - - +
60A LEU* 3.8 6.1 + - + +
176A TYR 3.6 13.7 - - - +
177A SER 4.1 5.2 - - - +
179A GLY* 4.5 7.2 - - - +
131B PHE* 3.4 39.5 - - + +
132B ASN* 3.8 23.8 - - - +
135B SER* 3.8 26.7 - - - +
136B ILE* 4.3 19.5 - - + -
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Residues in contact with ASN 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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47A LYS* 3.5 22.1 + - + +
48A LEU 3.8 3.6 - - - +
49A THR* 3.5 14.7 - - - +
57A ILE* 3.8 7.1 - - - +
58A MET* 1.3 82.1 - - - +
60A LEU* 1.3 67.4 + - - +
61A GLN* 3.5 3.4 - - - +
62A TYR* 3.9 16.8 + - + +
130A LYS* 4.8 0.5 + - - -
173A GLU* 2.9 33.1 + - - -
176A TYR* 2.9 33.2 + - - +
177A SER* 3.5 25.4 - - - +
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Residues in contact with LEU 60 (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 LEU* 2.8 29.0 + - + +
49A THR 3.9 12.8 - - - -
50A SER* 4.0 10.1 - - - +
58A MET* 4.0 10.8 - - + +
59A ASN* 1.3 73.7 - - - +
61A GLN* 1.3 55.9 + - + +
83A TYR* 3.5 42.2 - - + -
130A LYS* 2.7 27.6 + - - +
128B LEU* 3.5 49.6 - - + +
131B PHE* 3.6 20.9 - - + -
132B ASN* 4.1 6.1 - - + +
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Residues in contact with GLN 61 (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 LYS* 3.5 2.3 - - - +
48A LEU* 2.9 29.5 + - + +
59A ASN* 3.5 2.9 - - - -
60A LEU* 1.3 83.3 - - + +
62A TYR* 1.3 73.9 + - - +
63A TYR* 3.3 42.2 + - + -
67A PHE* 5.5 1.2 - - - -
123A GLN* 2.7 29.4 + - - +
126A TYR* 3.5 29.4 - - + +
127A SER* 4.2 1.0 + - - -
130A LYS* 3.7 14.6 - - - +
128B LEU* 3.7 13.6 - - + +
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Residues in contact with TYR 62 (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 ILE* 5.0 0.2 - - + -
46A THR 3.3 6.1 - - - +
47A LYS* 3.8 18.6 - - + -
59A ASN* 3.9 14.5 + - + -
61A GLN* 1.3 91.8 + - - +
63A TYR* 1.3 69.0 + - - +
64A LYS 4.3 0.4 - - - -
88A ILE* 3.7 31.9 - - + -
126A TYR* 5.0 4.7 + - - -
146A GLN* 3.6 29.2 - - + -
149A ILE* 6.0 1.6 - - + -
150A LEU* 4.1 18.6 - - + +
154A TYR* 3.8 21.3 - + + +
166A LEU* 4.9 11.0 - - + -
169A LEU* 4.5 13.9 - - - +
173A GLU* 4.3 10.8 + - - +
174A LEU* 5.8 0.5 - - - +
177A SER* 3.5 19.4 + - - -
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Residues in contact with TYR 63 (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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41A LEU* 3.6 11.5 - - + +
45A ILE* 3.4 3.8 - - - +
46A THR* 2.8 50.7 + - - +
48A LEU* 4.1 22.5 - - + +
61A GLN* 3.3 33.3 + - + +
62A TYR* 1.3 76.5 - - - +
64A LYS* 1.3 59.8 + - - +
67A PHE* 3.5 35.0 - + + -
68A VAL 4.4 1.0 + - - -
69A ILE* 3.9 31.0 - - + +
85A LEU* 4.2 13.7 - - + -
123A GLN* 2.4 35.2 + - - -
154A TYR* 4.4 2.9 - - - -
124B VAL* 5.8 0.2 - - - +
128B LEU* 5.0 3.8 - - - +
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Residues in contact with LYS 64 (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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41A LEU* 4.1 1.6 - - - -
44A GLY 3.5 9.9 - - - +
45A ILE* 4.5 8.3 - - + +
63A TYR* 1.3 73.6 - - - +
65A GLY* 1.3 76.9 + - - +
66A ALA 3.7 8.5 + - - +
67A PHE* 4.1 8.2 - - - +
153A VAL* 3.8 37.7 + - + +
154A TYR* 3.7 24.7 + - + +
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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