Contacts of the strand formed by residues 100 - 104 (chain A) in PDB entry 4LQL
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 100 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A VAL* 4.1 13.9 - - + -
78A THR* 3.4 31.6 - - - +
93A THR* 5.8 7.9 - - - -
96A LEU* 4.6 13.7 - - + -
98A LYS 3.8 1.4 + - - +
99A PRO* 1.3 72.5 - - - +
101A LEU* 1.3 61.0 + - - +
102A HIS* 4.2 8.0 + - + +
133A TYR* 6.4 2.0 - - + -
137A ASN* 4.2 25.4 - - + -
142A VAL* 4.8 6.7 - - + -
144A ALA* 3.5 20.5 + - + +
145A ALA* 2.7 34.8 + - - +
163A TRP* 4.6 2.8 + - - -
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Residues in contact with LEU 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A VAL 3.2 13.9 + - - +
77A ILE* 3.5 16.0 - - + +
78A THR 2.9 25.7 + - - +
99A PRO 4.2 0.2 + - - -
100A LEU* 1.3 74.2 - - - +
102A HIS* 1.3 61.4 + - - +
103A LEU* 3.7 6.6 + - + +
145A ALA* 3.3 24.7 - - + -
146A SER* 3.9 9.2 - - - +
147A VAL* 4.5 13.5 - - + +
160A ILE* 4.3 26.5 - - + -
163A TRP* 3.3 54.0 - - + -
461A GLN* 5.6 0.9 - - - +
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Residues in contact with HIS 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A THR* 3.1 19.3 - - - +
79A TRP* 5.5 0.9 - - - -
100A LEU* 4.1 11.1 + - + +
101A LEU* 1.3 70.7 - - - +
103A LEU* 1.3 64.9 + - - +
104A ALA* 3.9 4.7 + - + +
130A ASP* 5.0 14.6 - - + -
133A TYR* 4.4 22.0 - + + -
134A ALA* 5.8 2.5 - - + -
144A ALA* 6.5 0.2 - - + -
145A ALA 3.9 12.9 + - - +
146A SER* 3.4 28.5 + - - +
147A VAL 3.6 1.6 + - - -
440C MET* 6.1 5.2 - - + -
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Residues in contact with LEU 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A PHE* 6.2 3.4 - - + -
77A ILE* 6.4 1.6 - - + -
78A THR 3.4 5.6 + - - -
79A TRP* 3.3 26.1 - - + +
101A LEU* 3.7 10.1 + - + +
102A HIS* 1.3 73.7 - - - +
104A ALA* 1.3 59.5 + - - +
105A THR* 2.9 31.4 + - + -
130A ASP* 5.3 0.3 - - - +
147A VAL* 3.9 21.5 - - + +
148A TYR 5.8 0.2 - - - -
149A GLY 5.0 3.8 - - - +
151A TRP* 6.1 1.6 - - - -
156A VAL* 5.7 0.9 - - + +
160A ILE* 3.9 32.8 - - + -
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Residues in contact with ALA 104 (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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102A HIS* 3.9 5.6 + - + +
103A LEU* 1.3 70.5 - - - +
105A THR* 1.3 61.0 + - - +
126A SER* 5.9 0.9 - - - +
130A ASP* 4.4 23.1 - - + -
146A SER* 5.9 1.1 - - - +
147A VAL 3.2 19.0 + - - +
148A TYR* 4.3 15.6 - - + -
149A GLY 4.4 9.5 + - - -
436C ALA* 6.4 0.9 - - + -
440C MET* 5.4 12.3 - - + -
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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
------------------------------------------------------------
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