Contacts of the strand formed by residues 91 - 97 (chain B) 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 LEU 91 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31B MET* 4.6 3.3 - - - +
32B PRO 3.8 5.9 - - - +
35B ILE* 3.5 23.6 - - + +
37B ILE* 3.8 23.1 - - + -
76B LEU* 4.1 26.7 - - + +
79B ILE* 4.0 12.3 - - + -
80B ASN* 2.7 36.4 + - - +
86B LEU* 3.9 33.2 - - + -
89B ILE* 4.1 2.4 + - + +
90B THR* 1.3 73.2 - - - +
92B GLY* 1.3 58.7 + - - +
408B ALA* 3.9 16.6 - - + -
411B LEU* 4.0 19.1 - - + -
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Residues in contact with GLY 92 (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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31B MET* 3.1 20.6 - - - -
32B PRO 3.2 12.3 + - - -
33B GLY* 3.9 0.8 - - - -
35B ILE 2.7 13.6 + - - +
36B ILE* 3.8 5.8 - - - -
37B ILE* 2.9 22.9 + - - +
76B LEU* 3.8 6.1 - - - +
90B THR 3.7 1.6 + - - -
91B LEU* 1.3 74.9 - - - +
93B CYS* 1.3 62.8 + - - +
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Residues in contact with CYS 93 (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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29B ALA 4.4 1.3 - - - -
30B HIS* 3.6 5.2 + - - -
31B MET* 3.0 49.5 + - - +
36B ILE* 3.7 8.0 - - - +
37B ILE 3.1 13.9 - - - +
72B MET* 3.8 13.2 - - + -
73B LEU* 3.8 15.5 - - - -
76B LEU* 3.4 18.8 - - + -
92B GLY* 1.3 75.7 - - - +
94B GLU* 1.3 61.4 + - - +
95B ILE* 3.8 23.3 - - + -
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Residues in contact with GLU 94 (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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28B VAL* 3.6 17.5 - - + -
29B ALA 3.4 4.9 - - - -
30B HIS* 3.6 20.2 + - + +
36B ILE* 4.2 4.0 - - + +
37B ILE 3.0 7.0 + - - -
38B GLY* 3.5 1.7 - - - -
39B ALA 3.1 22.3 + - - -
93B CYS* 1.3 74.0 - - - +
95B ILE* 1.3 59.1 + - - +
96B ARG* 2.8 38.6 + - - +
111B GLU 4.1 7.1 - - - +
112B PHE* 3.5 17.6 - - + -
143B ILE* 4.1 22.1 - - + +
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Residues in contact with ILE 95 (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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28B VAL* 3.3 6.2 - - - +
29B ALA* 2.9 37.9 + - + +
39B ALA* 3.6 8.7 - - + +
41B PHE* 3.6 29.4 - - + -
69B VAL* 3.8 29.4 - - + +
72B MET* 3.6 31.0 - - + -
73B LEU* 3.7 33.9 - - + -
93B CYS* 3.8 9.6 - - + -
94B GLU* 1.3 72.6 - - - +
96B ARG* 1.3 65.6 + - - +
354B TRP* 3.5 8.6 - - + -
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Residues in contact with ARG 96 (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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26B ARG* 5.2 1.6 + - - +
27B VAL 5.0 0.7 - - - -
28B VAL* 3.5 30.3 - - + +
30B HIS* 5.3 2.2 - - - -
39B ALA 2.7 16.1 + - - +
40B LEU* 3.4 15.6 - - + -
41B PHE* 3.0 26.2 + - - +
43B VAL* 4.8 0.8 - - - +
94B GLU* 2.8 36.1 + - + +
95B ILE* 1.3 81.8 - - - +
97B ASP* 1.3 60.7 + - - +
108B GLN* 3.0 46.8 + - + +
111B GLU* 3.4 35.8 + - - +
112B PHE* 3.8 15.3 - - + -
354B TRP* 4.4 6.3 - - - -
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Residues in contact with ASP 97 (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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26B ARG* 4.4 19.8 + - + +
27B VAL 4.8 1.2 + - - +
40B LEU* 5.1 0.9 - - - -
41B PHE 3.4 3.8 - - - -
43B VAL* 3.1 23.8 + - - -
44B HIS* 2.5 38.6 + - - -
57B CYS* 5.0 0.2 - - - +
96B ARG* 1.3 71.6 - - - +
98B SER* 1.3 60.4 + - - +
99B CYS* 3.0 32.4 + - - -
104B VAL* 3.4 15.1 - - - +
108B GLN* 3.5 16.0 + - - +
354B TRP* 4.2 17.3 + - + +
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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