Contacts of the strand formed by residues 71 - 78 (chain V) in PDB entry 1LM8
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 PRO 71 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69V ARG 3.3 11.2 - - - +
70V GLU* 1.3 84.9 - - - +
72V SER* 1.3 59.8 + - - +
110V HIS* 6.0 6.3 - - + -
111V SER 3.5 8.7 - - - +
112V TYR* 3.5 14.9 - - + -
140V LEU* 4.3 10.7 - - - +
141V ASN* 4.6 4.8 + - - +
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Residues in contact with SER 72 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70V GLU 3.6 0.2 + - - -
71V PRO* 1.3 75.3 - - - +
73V GLN* 1.3 64.0 + - - +
74V VAL* 3.6 3.5 + - - +
110V HIS* 5.2 0.7 - - - -
111V SER* 2.8 33.5 + - - -
112V TYR 4.0 1.6 - - - -
113V ARG 3.9 18.6 - - - -
138V PRO* 3.6 18.4 - - - +
139V SER 2.5 30.0 + - - -
140V LEU* 5.0 0.9 - - - -
141V ASN* 3.7 10.8 + - - -
147V ILE* 4.0 4.5 - - - +
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Residues in contact with GLN 73 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71V PRO 4.3 0.2 - - - -
72V SER* 1.3 71.4 - - - +
74V VAL* 1.3 64.3 + - - +
108V ARG* 2.6 43.8 + - + +
109V ILE 3.8 7.0 + - - +
110V HIS* 2.9 35.9 + - - +
141V ASN* 2.7 28.2 + - - +
144V GLY 5.9 1.8 - - - +
146V PRO* 4.0 18.8 - - + -
147V ILE* 2.9 23.0 + - - +
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Residues in contact with VAL 74 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72V SER* 3.8 13.0 - - - +
73V GLN* 1.3 81.4 - - - +
75V ILE* 1.3 69.1 + - - +
76V PHE* 3.8 22.9 - - + -
108V ARG* 3.5 4.0 - - - +
109V ILE* 2.6 48.0 + - + +
111V SER* 4.3 5.4 - - - -
117V TRP* 6.0 0.2 - - - +
136V PHE* 3.6 34.8 - - + -
138V PRO* 4.0 19.7 - - + -
146V PRO* 4.7 0.2 - - - -
147V ILE* 3.3 16.6 - - + +
149V ALA* 4.3 0.4 - - + -
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Residues in contact with ILE 75 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572H PHE* 3.7 30.3 - - + -
73V GLN* 5.9 0.2 - - + -
74V VAL* 1.3 83.2 - - - +
76V PHE* 1.3 63.3 + - - +
77V CYS* 3.6 23.6 + - - -
107V ARG 3.4 5.4 - - - +
108V ARG* 4.2 18.6 - - + -
146V PRO* 3.5 32.1 - - + -
147V ILE 2.9 8.0 + - - +
148V PHE* 3.7 22.9 - - + -
149V ALA* 2.9 26.0 + - - +
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Residues in contact with PHE 76 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566H ILE* 6.2 0.4 - - + -
74V VAL* 3.8 20.2 - - + -
75V ILE* 1.3 70.7 - - - +
77V CYS* 1.3 59.8 + - - +
86V PRO* 3.6 35.9 - - + -
98V TYR* 5.6 1.6 - + + -
101V LEU* 3.5 22.2 - - + +
106V GLY* 3.1 4.2 - - - -
107V ARG* 2.9 36.3 + - + +
109V ILE* 3.6 30.7 - - + -
111V SER* 6.4 0.4 - - - -
117V TRP* 3.8 40.8 - + - -
119V PHE* 3.8 17.9 - + - -
136V PHE* 4.6 4.7 - + - -
149V ALA* 3.8 18.4 - - + -
151V ILE* 4.2 4.9 - - + -
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Residues in contact with CYS 77 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572H PHE* 5.1 1.3 - - - -
574H LEU* 4.0 18.6 - - + -
75V ILE* 3.6 18.8 - - - -
76V PHE* 1.3 71.0 - - - +
78V ASN* 1.3 61.2 + - - +
79V ARG* 3.1 32.1 + - - +
105V THR 4.0 3.6 - - - -
106V GLY* 4.3 0.7 - - - -
148V PHE* 3.6 34.3 - - - -
149V ALA 2.9 10.9 + - - +
150V ASN* 3.7 5.2 - - - +
151V ILE* 2.9 31.3 + - - +
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Residues in contact with ASN 78 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574H LEU* 3.0 11.4 - - - +
76V PHE 4.1 1.2 - - - -
77V CYS* 1.3 69.0 - - - +
79V ARG* 1.3 56.2 + - - +
80V SER* 2.7 26.7 + - - -
82V ARG 2.8 25.2 + - - -
84V VAL* 3.3 16.0 - - + +
101V LEU* 3.1 32.0 + - + +
102V PRO 3.1 15.3 + - - +
103V PRO* 3.4 3.7 - - - +
104V GLY* 3.0 22.0 + - - -
105V THR 2.9 19.8 + - - +
151V ILE* 4.2 6.6 - - + +
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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