Contacts of the strand formed by residues 121 - 126 (chain A) in PDB entry 1LC7
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 GLU 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A ARG 2.7 18.7 + - - +
100A ARG* 3.3 24.2 + - + +
101A ALA 3.0 25.3 + - - +
119A GLY 4.1 0.4 + - - -
120A CYS* 1.3 70.1 - - - +
122A ILE* 1.3 64.8 + - - +
123A ARG* 3.0 32.7 + - - +
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Residues in contact with ILE 122 (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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101A ALA 3.5 5.8 - - - +
103A ILE* 4.1 20.9 - - + -
112A GLY* 3.9 17.9 - - - +
115A LEU* 3.7 32.8 - - + -
116A ALA* 3.9 13.5 - - + +
120A CYS* 3.4 13.6 + - - +
121A GLU* 1.3 77.1 - - - +
123A ARG* 1.3 72.9 + - - +
124A ARG* 3.7 42.4 + - - +
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Residues in contact with ARG 123 (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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100A ARG* 3.5 19.9 - - - +
101A ALA 2.8 12.4 + - - +
102A MET* 3.2 21.6 - - + +
103A ILE 3.1 24.1 + - - +
121A GLU* 3.0 27.2 + - - +
122A ILE* 1.3 79.2 - - - +
124A ARG* 1.3 63.4 + - - +
144A THR* 3.5 9.9 + - - -
146A ASP* 2.6 44.0 + - - -
147A LEU* 4.0 21.1 - - - +
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Residues in contact with ARG 124 (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 MET* 4.8 3.2 - - - +
103A ILE* 3.5 25.8 - - + +
105A THR* 3.9 26.6 - - + +
112A GLY* 5.7 3.0 - - - -
122A ILE* 3.7 44.0 + - + +
123A ARG* 1.3 76.2 - - - +
125A TRP* 1.3 62.2 + - - +
126A SER* 3.6 8.1 + - - +
329A PRO* 5.4 10.7 - - - +
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Residues in contact with TRP 125 (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 MET* 3.9 20.8 - - + +
103A ILE 2.8 16.0 + - - +
104A VAL* 3.2 11.4 - - + +
105A THR* 3.0 23.2 + - - -
123A ARG 4.0 0.4 + - - -
124A ARG* 1.3 72.8 - - - +
126A SER* 1.3 75.7 + - - +
127A LEU* 3.7 5.8 + - + +
135A LEU* 4.0 16.8 - - + +
136A THR* 4.7 6.5 + - - +
138A ALA* 3.6 29.4 - - + -
139A ILE* 3.6 43.5 - - + +
142A ALA* 3.6 29.4 - - + -
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Residues in contact with SER 126 (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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105A THR* 3.8 14.7 + - - -
124A ARG* 3.6 8.9 + - - +
125A TRP* 1.3 88.9 + - - +
127A LEU* 1.3 68.2 + - - +
128A ARG* 3.7 11.7 + - - +
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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