Contacts of the strand formed by residues 85 - 93 (chain A) in PDB entry 4LML
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 ASP 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83A ALA 3.7 2.5 + - - +
84A ARG* 1.3 70.2 - - - +
86A ALA* 1.3 68.8 + - - +
87A ASP* 5.0 3.3 - - - +
105A PHE* 3.2 6.2 - - - +
106A SER* 3.1 48.5 + - - +
82C ASN* 5.9 2.4 - - - +
83C ALA* 4.8 15.9 - - - +
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Residues in contact with ALA 86 (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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84A ARG* 3.9 14.6 + - - +
85A ASP* 1.3 82.7 + - - +
87A ASP* 1.3 71.3 + - - +
88A VAL* 5.9 0.6 - - - +
103A GLU* 4.0 28.7 - - - +
104A ARG 3.6 8.1 - - - +
105A PHE* 4.5 0.2 - - + -
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Residues in contact with ASP 87 (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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85A ASP* 5.0 5.2 - - - +
86A ALA* 1.3 83.2 - - - +
88A VAL* 1.3 66.9 - - - +
89A VAL* 3.2 4.2 + - + +
103A GLU* 3.5 3.6 - - - +
104A ARG* 3.2 34.0 + - + +
76C ARG* 6.2 4.3 - - - -
83C ALA* 4.5 15.8 - - - +
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Residues in contact with VAL 88 (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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66A GLU* 5.2 6.4 - - - +
67A PRO* 3.6 37.0 - - + -
87A ASP* 1.3 73.5 - - - +
89A VAL* 1.3 64.1 + - - +
90A ASP 4.2 6.3 - - - +
91A ILE* 3.9 20.9 - - + +
101A TYR* 4.0 21.3 - - + +
102A LEU 4.5 0.9 - - - +
103A GLU* 4.4 5.2 - - - +
74C GLU* 4.1 8.8 - - - +
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Residues in contact with VAL 89 (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 PHE* 3.9 21.5 - - + -
87A ASP* 3.2 5.0 + - + +
88A VAL* 1.3 77.4 - - - +
90A ASP* 1.3 67.8 + - + +
102A LEU* 3.0 38.2 + - + +
104A ARG* 4.1 15.7 - - + +
74C GLU* 3.8 16.8 - - - +
76C ARG* 4.1 22.7 - - - +
132C ARG* 3.7 22.0 - - + -
134C VAL* 6.0 0.5 - - - +
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Residues in contact with ASP 90 (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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64A THR* 4.0 8.0 - - - +
88A VAL* 3.7 1.4 - - - +
89A VAL* 1.3 88.5 - - + +
91A ILE* 1.3 77.2 + - - +
92A SER* 3.1 26.2 + - - -
100A GLN 3.7 1.4 - - - +
101A TYR* 3.6 0.7 - - - -
102A LEU* 2.9 38.9 + - + +
132C ARG* 4.9 6.8 + - - +
133C SER 5.4 0.7 - - - -
134C VAL* 4.0 19.8 - - - +
178C ARG* 3.6 23.0 + - - -
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Residues in contact with ILE 91 (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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64A THR* 3.1 11.2 - - - +
65A TYR* 3.0 47.3 + - + +
66A GLU 4.4 0.2 - - - -
67A PRO* 3.6 33.0 - - + -
70A ILE* 4.7 2.5 - - + -
72A ILE* 3.6 19.3 - - + -
88A VAL* 3.9 9.6 - - + +
90A ASP* 1.3 83.1 + - - +
92A SER* 1.3 59.6 + - - +
93A VAL* 4.7 1.3 - - + -
99A VAL* 3.6 29.2 - - + -
100A GLN 3.4 3.4 - - - +
101A TYR* 3.5 26.9 - - + -
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Residues in contact with SER 92 (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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62A VAL* 3.6 15.6 - - - +
63A LYS 3.8 3.8 - - - -
64A THR* 3.5 15.0 + - - +
90A ASP* 3.1 23.5 + - - -
91A ILE* 1.3 71.8 - - - +
93A VAL* 1.3 63.8 + - - +
94A SER* 3.5 1.6 + - - -
100A GLN* 2.8 47.4 + - - +
178C ARG* 3.6 16.9 + - - -
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Residues in contact with VAL 93 (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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51A LEU* 3.5 33.4 - - + +
61A ARG 4.6 0.2 - - - +
62A VAL* 3.3 4.3 - - - +
63A LYS* 2.7 39.3 + - + +
65A TYR* 3.3 31.0 - - + -
70A ILE* 4.7 1.3 - - + -
91A ILE* 4.7 2.5 - - + -
92A SER* 1.3 70.7 - - - +
94A SER* 1.3 76.9 + - - +
97A GLY* 4.3 5.6 - - - -
98A THR 3.4 11.4 - - - +
99A VAL* 3.6 23.6 - - + +
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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