Contacts of the strand formed by residues 85 - 93 (chain A) in PDB entry 3LQM
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 HIS 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A TYR* 5.2 2.0 - + + -
57A LEU 4.8 13.0 - - - -
79A LEU* 3.7 29.9 - - + +
80A SER* 2.8 55.7 + - - -
83A GLY* 3.6 16.1 + - - -
84A ASP* 1.3 76.5 - - - +
86A THR* 1.3 63.7 + - - +
87A LEU* 4.2 16.6 - - + -
104A THR* 3.2 6.8 - - - -
105A PHE* 2.8 43.5 + - + +
107A PRO* 3.8 11.1 - - + +
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Residues in contact with THR 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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56A TYR* 3.4 3.3 - - - -
57A LEU* 3.0 54.5 + - + +
62A PHE* 3.8 9.8 - - + -
84A ASP 5.0 1.6 + - - -
85A HIS* 1.3 76.9 + - - +
87A LEU* 1.3 63.9 + - - +
102A GLN* 3.3 41.5 - - + +
103A ILE 3.5 6.3 - - - +
104A THR* 4.2 12.0 - - + +
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Residues in contact with LEU 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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29A MET* 3.4 33.0 - - + -
38A LEU* 4.6 6.3 - - + -
55A GLN 3.2 7.0 - - - +
56A TYR* 3.4 24.2 - - + -
62A PHE* 4.8 1.1 - - - -
76A PHE* 4.0 16.6 - - + -
79A LEU* 3.8 23.6 - - + -
85A HIS* 4.2 7.9 - - + -
86A THR* 1.3 87.3 - - - +
88A ARG* 1.3 63.0 + - - +
102A GLN* 3.2 5.5 - - - +
103A ILE* 2.8 53.9 + - + +
105A PHE* 4.5 9.6 - - + -
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Residues in contact with ARG 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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38A LEU* 5.0 2.9 - - - -
53A THR 3.9 0.3 - - - +
54A ALA* 3.2 3.6 - - - +
55A GLN* 2.7 69.3 + - + +
62A PHE* 3.2 51.9 - - + +
87A LEU* 1.3 76.6 - - - +
89A VAL* 1.3 61.0 + - - +
100A TRP* 3.4 52.2 - - + +
101A VAL 3.1 12.8 - - - +
102A GLN* 4.0 17.3 - - + +
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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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24A PRO* 4.1 13.1 - - + +
27A VAL* 4.0 33.7 - - + -
38A LEU* 4.0 13.9 - - + -
40A TRP* 4.1 22.7 - - + -
52A PHE* 4.2 6.7 - - + -
53A THR 3.1 19.3 - - - +
54A ALA* 4.1 7.6 - - + -
88A ARG* 1.3 76.7 - - - +
90A ARG* 1.3 70.2 + - - +
100A TRP* 3.6 3.8 - - - -
101A VAL* 2.9 36.2 + - + +
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Residues in contact with ARG 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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24A PRO* 3.7 8.7 - - - -
52A PHE* 3.2 6.6 - - - +
53A THR* 2.9 33.3 + - - +
89A VAL* 1.3 75.8 - - - +
91A ALA* 1.3 63.9 + - - +
92A GLU* 3.3 26.4 + - - +
97A HIS* 3.4 34.8 + - - +
98A SER* 3.4 25.7 + - - +
99A ASP 3.4 9.6 - - - +
100A TRP* 3.5 47.5 - - + +
608A SO4 2.8 41.2 + - - -
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Residues in contact with ALA 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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21A VAL* 3.9 9.0 - - + -
22A PRO 3.5 24.0 - - - +
23A PRO 4.8 0.2 - - - -
24A PRO* 3.7 6.0 - - + +
43A PRO* 5.0 0.2 - - + -
50A LEU* 4.5 10.1 - - + -
51A THR 3.4 5.8 - - - +
52A PHE* 3.6 22.2 - - + -
90A ARG* 1.3 74.1 - - - +
92A GLU* 1.3 64.4 + - - +
97A HIS* 3.3 3.6 - - - +
98A SER* 2.8 30.4 + - - -
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Residues in contact with GLU 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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21A VAL* 4.6 1.1 - - - -
49A GLN 4.3 0.3 - - - +
50A LEU* 3.5 8.1 - - - +
51A THR* 2.8 45.2 + - - +
53A THR* 2.9 28.2 + - - +
68A GLN* 3.5 25.0 + - - +
90A ARG* 3.3 33.5 + - + +
91A ALA* 1.3 81.8 - - - +
93A PHE* 1.3 64.2 + - - +
94A ALA 5.4 2.7 - - - +
96A GLU 3.5 9.9 - - - +
97A HIS* 4.0 10.3 - - + +
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Residues in contact with PHE 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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21A VAL* 4.2 7.5 - - + +
45A PHE* 3.6 24.0 - + + -
47A LYS* 3.4 37.0 - - + -
48A GLY* 3.7 21.3 - - - -
49A GLN 3.5 20.2 - - - -
50A LEU* 4.0 11.0 - - + -
92A GLU* 1.3 75.9 - - - +
94A ALA* 1.3 86.5 + - + +
96A GLU* 2.9 35.7 + - - +
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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