Contacts of the strand formed by residues 91 - 95 (chain U) in PDB entry 4QLC
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 GLY 91 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85I T 3.9 11.9 - - - -
86I G 3.5 11.0 - - - +
46U SER* 3.2 24.9 - - - -
47U ARG* 3.7 4.9 + - - +
48U GLN* 4.7 0.8 - - - +
85U LYS 3.3 13.7 - - - -
88U GLY 3.8 1.3 + - - -
89U ALA 3.4 5.1 + - - -
90U SER* 1.3 75.3 - - - +
92U SER* 1.3 59.3 + - - -
93U PHE* 3.8 10.3 - - - -
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Residues in contact with SER 92 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86I G 3.0 18.4 + - - -
43U GLY* 3.5 18.5 + - - -
45U SER 3.2 12.3 - - - -
46U SER* 4.3 5.2 - - - -
84U THR* 2.9 25.0 + - - +
85U LYS* 3.0 33.9 + - - +
91U GLY* 1.3 72.8 - - - -
93U PHE* 1.3 63.7 + - - +
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Residues in contact with PHE 93 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36U ILE* 4.6 4.5 - - + +
43U GLY 3.8 0.4 + - - -
44U GLY* 3.2 2.2 - - - -
45U SER* 2.6 46.3 + - - +
46U SER 4.0 13.7 - - - -
47U ARG 4.0 0.9 - - - -
50U ILE* 4.9 5.6 - - + -
72U ILE* 4.0 33.0 - - + -
76U LEU* 4.6 6.3 - - + -
81U LEU* 4.0 24.0 - - + -
82U LYS 3.1 14.6 - - - +
83U GLN* 4.2 16.8 - - + -
84U THR* 3.4 7.6 - - - +
88U GLY 3.2 23.1 - - - -
89U ALA 3.6 21.5 - - - -
91U GLY* 3.8 23.3 - - - -
92U SER* 1.3 76.2 - - - +
94U ARG* 1.3 59.9 + - - +
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Residues in contact with ARG 94 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163J C 3.1 23.8 + - - -
164J C 2.8 57.0 + - - -
165J A 5.5 0.2 + - - -
36U ILE* 4.7 4.7 - - + -
42U ARG* 3.7 27.2 + - - +
44U GLY* 4.3 13.0 - - - -
81U LEU* 3.2 10.4 - - - +
82U LYS* 2.6 70.7 + - + +
83U GLN 5.1 2.8 + - - +
84U THR* 3.9 26.2 + - - +
93U PHE* 1.3 74.2 - - - +
95U LEU* 1.3 63.7 + - - +
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Residues in contact with LEU 95 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164J C 5.9 1.0 - - - +
33U ALA* 4.0 20.2 - - + +
36U ILE* 4.1 21.2 - - + +
37U ARG* 3.4 57.2 - - + +
80U VAL* 3.9 26.7 - - + +
81U LEU* 4.3 10.8 - - + -
82U LYS* 4.4 1.3 - - - +
94U ARG* 1.3 91.3 - - - +
96U ALA* 1.3 68.0 + - - +
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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