Contacts of the strand formed by residues 35 - 41 (chain A) in PDB entry 3LMK
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 35 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A ASP* 1.3 84.9 - - - +
36A ILE* 1.3 63.6 + - - +
37A ILE* 3.8 18.2 - - + +
86A LEU* 4.8 0.7 - - + -
89A ILE* 3.8 26.9 - - + -
90A THR 3.3 2.8 + - - -
91A LEU* 3.5 15.0 - - + -
92A GLY 2.9 24.3 + - - +
144A VAL* 4.3 10.5 - - + -
411A LEU* 4.0 25.4 - - + -
425A LEU* 3.9 19.5 - - + -
429A MET* 4.5 4.7 - - + -
432A ILE* 3.7 33.9 - - + -
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Residues in contact with ILE 36 (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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31A MET 4.8 6.5 - - - +
32A PRO* 5.5 2.0 - - + -
33A GLY 4.6 13.0 - - - +
35A ILE* 1.3 75.8 - - - +
37A ILE* 1.3 64.2 + - - +
92A GLY* 3.6 10.3 - - - -
93A CYS 3.7 24.7 - - - +
94A GLU* 3.9 7.0 - - + +
141A LYS* 3.8 35.6 - - + +
142A PRO 4.0 13.0 + - - +
143A ILE* 3.4 24.5 - - + -
144A VAL* 3.1 32.3 + - - +
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Residues in contact with ILE 37 (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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35A ILE* 3.8 10.1 - - + +
36A ILE* 1.3 80.3 - - - +
38A GLY* 1.3 72.6 + - - +
72A MET* 3.8 19.7 - - + -
76A LEU* 5.5 2.7 - - + -
91A LEU* 3.7 34.3 - - + -
92A GLY 3.0 13.1 + - - +
93A CYS* 3.0 9.0 - - - +
94A GLU 2.9 22.5 + - - -
143A ILE* 4.6 0.2 - - - -
144A VAL* 5.5 1.3 - - + -
145A GLY 3.7 13.5 - - - +
147A ILE* 4.0 13.9 - - + -
404A ILE* 6.0 1.3 - - + -
407A MET* 3.8 25.8 - - + -
411A LEU* 3.8 13.2 - - + -
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Residues in contact with GLY 38 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A ILE* 1.3 80.9 - - - +
39A ALA* 1.3 61.1 + - - +
94A GLU 3.3 10.1 - - - -
112A PHE* 4.0 16.6 - - - -
143A ILE* 3.7 10.7 - - - +
145A GLY 2.7 16.7 + - - -
146A VAL* 3.3 5.2 - - - -
147A ILE* 2.8 22.9 + - - -
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Residues in contact with ALA 39 (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 GLY* 1.3 76.9 - - - +
40A LEU* 1.3 62.2 + - - +
41A PHE* 3.7 27.8 - - + -
72A MET* 3.7 20.2 - - + -
94A GLU 2.9 6.3 + - - +
95A ILE* 4.2 10.3 - - + -
96A ARG* 2.8 31.2 + - - +
112A PHE* 3.7 5.2 - - - -
146A VAL* 4.8 0.4 - - - -
147A ILE* 3.2 10.3 - - + +
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Residues in contact with LEU 40 (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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39A ALA* 1.3 78.0 - - - +
41A PHE* 1.3 65.3 + - - +
96A ARG* 3.4 26.7 - - + +
98A SER* 4.4 14.8 - - - +
105A ALA* 4.6 5.4 - - + +
108A GLN* 4.3 14.1 - - + -
109A SER* 3.8 20.2 - - - +
112A PHE* 4.0 15.5 - - + -
146A VAL* 4.3 6.1 - - + -
147A ILE 2.8 14.1 + - - +
149A PRO* 3.8 30.7 - - + +
158A VAL* 3.9 26.0 - - + -
172A TYR* 3.0 17.5 + - - -
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Residues in contact with PHE 41 (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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39A ALA* 3.7 24.0 - - + -
40A LEU* 1.3 75.3 - - - +
42A SER* 1.3 61.5 + - - +
43A VAL* 3.1 17.4 + - + +
64A TYR 4.0 9.6 - - - +
65A GLY 4.5 2.2 - - - +
68A ARG* 3.7 35.7 - - + -
69A VAL* 3.8 11.4 - - + -
72A MET* 3.7 26.9 - - + -
95A ILE* 3.6 22.2 - - + -
96A ARG 3.1 6.7 + - - -
97A ASP* 3.3 6.1 - - - +
98A SER* 2.9 24.2 + - - -
147A ILE* 4.5 5.2 - - + -
172A TYR* 3.2 36.8 - + - -
400A VAL* 4.2 13.7 - - + -
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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