Contacts of the strand formed by residues 132 - 140 (chain B) in PDB entry 5LS6
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 132 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A GLN* 2.8 28.8 + - - +
86B ASN* 3.8 11.6 - - + +
88B LEU* 3.6 34.2 - - + +
113B PHE* 4.2 8.7 - - + -
124B TYR* 3.7 32.7 - - + -
125B GLU 3.5 5.2 - - - +
126B CYS* 4.5 7.4 - - - -
130B GLY 3.2 7.2 + - - +
131B GLU* 1.3 77.6 - - - +
133B ARG* 1.3 55.8 + - - +
134B LEU 3.7 0.2 + - - -
426B ILE* 4.3 11.0 - - + -
434B ILE* 5.2 4.3 - - + +
436B ARG* 3.5 42.8 - - + +
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Residues in contact with ARG 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A ILE* 5.3 6.2 - - + +
94A GLN* 3.5 7.0 - - - +
124B TYR* 3.4 4.7 - - - +
125B GLU* 2.7 42.6 + - - +
127B HIS* 3.2 39.9 + - + +
131B GLU* 3.1 36.1 + - - +
132B ILE* 1.3 74.0 - - - +
134B LEU* 1.3 67.3 + - - +
135B LEU* 3.5 17.6 - - + +
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Residues in contact with LEU 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A ILE* 4.9 2.4 - - - +
83A CYS* 3.8 17.3 - - + +
85A VAL* 4.0 19.1 - - + -
94A GLN* 2.5 39.3 + - + +
96A ILE* 3.3 43.1 - - + +
122B THR* 3.4 22.2 - - + -
123B LEU 4.2 0.7 - - - +
124B TYR* 3.3 33.9 - - + -
132B ILE 3.7 0.2 + - - -
133B ARG* 1.3 75.1 - - - +
135B LEU* 1.3 63.8 + - - +
136B GLN 4.2 4.7 - - - +
137B SER* 5.1 2.0 - - - -
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Residues in contact with LEU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A VAL* 3.4 42.6 - - + +
69A HIS 5.2 1.1 - - - +
70A ILE* 3.4 37.5 - - + +
71A LEU 4.8 1.2 + - - +
96A ILE* 3.6 13.7 - - - +
112B VAL* 4.0 13.2 - - + -
123B LEU* 2.9 23.2 + - + +
124B TYR 4.0 0.2 - - - -
125B GLU* 3.3 40.4 - - + +
133B ARG* 3.5 19.1 - - + +
134B LEU* 1.3 74.6 - - - +
136B GLN* 1.3 72.2 + - + +
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Residues in contact with GLN 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A HIS 3.5 18.9 + - - +
70A ILE* 4.9 2.7 - - - -
71A LEU 4.9 5.1 - - - +
96A ILE* 4.4 8.3 - - - -
122B THR* 3.4 4.9 - - - +
123B LEU* 2.8 41.4 + - + +
134B LEU* 3.9 1.5 - - - +
135B LEU* 1.3 87.3 - - - +
137B SER* 1.3 62.1 + - - +
138B TYR* 3.5 31.2 + - + +
177B PRO* 3.0 35.9 + - - +
180B MET* 3.7 27.5 - - + +
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Residues in contact with SER 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A CYS* 4.0 12.9 - - - -
96A ILE* 4.2 9.6 - - - +
97A PRO 4.2 1.9 - - - +
98A LEU* 3.4 24.8 - - - +
99A LYS* 3.0 24.9 + - - +
120B ARG* 4.2 4.7 - - - -
121B VAL 3.0 12.2 + - - -
122B THR* 2.9 30.1 + - - +
134B LEU* 5.1 1.1 - - - -
136B GLN* 1.3 77.9 - - - +
138B TYR* 1.3 62.4 + - - +
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Residues in contact with TYR 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A LYS* 3.3 32.8 - - + +
101A LEU* 3.6 31.5 - - + +
120B ARG* 3.1 4.4 - - - +
121B VAL* 2.7 56.6 + - + +
123B LEU* 4.4 15.3 - - + -
136B GLN* 3.5 34.3 + - + -
137B SER* 1.3 76.9 + - - +
139B VAL* 1.3 62.9 + - - +
140B ASP 4.3 0.3 + - - -
147B PHE* 5.1 0.2 - - - -
175B ILE* 3.5 22.7 - - + -
177B PRO* 3.5 26.5 - - - +
180B MET* 3.6 25.6 - - + -
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Residues in contact with VAL 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A LEU* 3.4 37.2 - - + +
99A LYS 2.8 12.6 + - - +
100A THR* 3.6 5.6 - - + +
101A LEU* 3.0 26.7 + - - -
119B ASN* 3.3 27.8 - - - +
120B ARG* 3.7 28.9 - - + +
138B TYR* 1.3 71.5 - - - +
140B ASP* 1.3 69.4 + - - +
141B ALA* 3.3 2.6 + - - -
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Residues in contact with ASP 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A LEU* 3.7 9.4 - - - +
104A VAL* 5.2 0.2 - - - +
119B ASN* 3.0 25.6 + - + +
138B TYR 4.3 0.6 + - - -
139B VAL* 1.3 71.5 - - - +
141B ALA* 1.3 61.8 + - - +
142B ASP* 2.9 48.9 + - - +
145B GLU* 3.6 28.1 - - + +
147B PHE* 3.4 16.2 - - + -
169B ARG* 4.4 3.6 + - - -
173B ARG* 2.5 45.4 + - - -
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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