Contacts of the strand formed by residues 91 - 97 (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 LEU 91 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A MET* 4.2 4.2 - - - +
32A PRO 3.8 4.9 - - - +
35A ILE* 3.5 20.0 - - + +
37A ILE* 3.7 24.7 - - + -
76A LEU* 3.7 39.4 - - + +
79A ILE* 3.8 16.2 - - + -
80A ASN* 3.0 30.4 + - - +
86A LEU* 3.7 34.3 - - + -
89A ILE* 3.8 7.6 + - + +
90A THR* 1.3 70.8 - - - +
92A GLY* 1.3 60.7 + - - +
404A ILE 5.8 0.4 - - - +
408A ALA* 4.1 13.5 - - + +
411A LEU* 4.0 5.8 - - + -
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Residues in contact with GLY 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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31A MET* 3.0 19.3 - - - -
32A PRO 3.3 12.6 + - - -
33A GLY* 3.8 2.1 - - - -
35A ILE 2.9 11.4 + - - +
36A ILE* 4.0 4.0 - - - -
37A ILE* 3.0 24.1 + - - +
76A LEU* 3.5 8.8 - - - +
90A THR 3.8 1.8 + - - -
91A LEU* 1.3 74.3 - - - +
93A CYS* 1.3 63.3 + - - +
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Residues in contact with CYS 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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29A ALA 4.5 1.8 - - - -
30A HIS* 3.7 6.9 + - - -
31A MET* 2.8 50.0 + - - +
36A ILE* 3.7 9.1 - - - +
37A ILE 3.0 13.9 - - - +
72A MET* 3.8 12.1 - - + -
73A LEU* 4.2 8.5 - - - -
76A LEU* 3.7 16.2 - - + -
92A GLY* 1.3 75.7 - - - +
94A GLU* 1.3 60.6 + - - +
95A ILE* 3.6 31.0 - - + -
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Residues in contact with GLU 94 (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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28A VAL* 3.8 20.4 - - + -
29A ALA 3.6 2.9 - - - -
30A HIS* 3.8 16.8 + - + +
36A ILE* 3.9 7.2 - - + +
37A ILE 2.9 5.7 + - - -
38A GLY* 3.3 2.1 - - - -
39A ALA 2.9 23.1 + - - -
93A CYS* 1.3 74.2 - - - +
95A ILE* 1.3 60.7 + - - +
96A ARG* 3.3 30.7 + - - +
111A GLU 4.0 8.5 - - - +
112A PHE* 3.6 18.5 - - + -
141A LYS 5.2 3.1 - - - +
143A ILE* 3.9 29.3 - - + +
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Residues in contact with ILE 95 (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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28A VAL* 3.4 5.4 - - - +
29A ALA* 2.9 39.7 + - + +
39A ALA* 3.6 8.5 - - + +
41A PHE* 3.6 27.6 - - + -
43A VAL* 5.6 0.2 - - + -
69A VAL* 3.9 22.4 - - + +
72A MET* 3.5 37.7 - - + -
73A LEU* 3.9 18.2 - - + -
93A CYS* 3.6 20.6 - - + -
94A GLU* 1.3 76.0 - - - +
96A ARG* 1.3 63.6 + - - +
354A TRP* 3.4 12.9 - - + -
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Residues in contact with ARG 96 (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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25A ARG* 6.0 2.6 - - - +
26A ARG* 4.6 3.4 + - - +
27A VAL 5.0 1.1 - - - +
28A VAL* 3.3 36.4 - - + +
30A HIS* 5.3 1.8 - - - -
39A ALA 2.8 12.2 + - - +
40A LEU* 3.4 17.3 - - + -
41A PHE* 3.1 24.9 + - - +
43A VAL* 4.9 0.6 - - - +
94A GLU* 3.3 29.7 + - - -
95A ILE* 1.3 81.8 - - - +
97A ASP* 1.3 60.7 + - - +
108A GLN* 2.7 57.2 + - + +
111A GLU* 3.3 31.8 + - - +
112A PHE* 3.6 17.8 - - + -
354A TRP* 4.5 5.4 - - - -
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Residues in contact with ASP 97 (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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26A ARG* 4.1 17.4 + - + +
27A VAL 4.8 1.2 + - - -
40A LEU* 4.7 0.9 - - - -
41A PHE 3.4 3.1 - - - -
43A VAL* 3.0 31.9 + - + -
44A HIS* 2.7 34.4 + - - -
96A ARG* 1.3 71.5 - - - +
98A SER* 1.3 59.2 + - - +
99A CYS* 3.0 29.8 + - - -
104A VAL* 3.5 8.3 - - - +
108A GLN* 3.3 25.6 + - - +
354A TRP* 4.3 14.4 + - + +
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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