Contacts of the strand formed by residues 101 - 108 (chain A) in PDB entry 1IQ0
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 ARG 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A PRO* 4.2 7.7 + - + +
100A ARG* 1.3 87.5 - - - +
102A PRO* 1.3 74.0 - - + +
103A GLY 4.4 0.5 - - - +
139A ALA* 2.8 34.4 + - - +
140A GLY 2.8 15.3 + - - +
141A ARG* 3.4 38.8 + - - +
142A GLU* 3.8 9.5 + - - +
517A LEU* 5.5 3.0 - - - +
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Residues in contact with PRO 102 (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* 4.0 12.8 - - + +
101A ARG* 1.3 91.5 - - + +
103A GLY* 1.3 61.1 + - - +
141A ARG* 5.0 5.0 + - - -
142A GLU* 4.2 7.2 - - - +
347A GLU* 5.0 1.5 - - - +
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Residues in contact with GLY 103 (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 ARG 4.4 0.3 - - - +
102A PRO* 1.3 78.3 - - - +
104A VAL* 1.3 66.6 + - - +
105A VAL* 3.5 2.3 + - - +
141A ARG* 4.1 12.6 + - - -
142A GLU* 3.4 23.3 + - - +
347A GLU* 3.4 26.9 - - - -
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Residues in contact with VAL 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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103A GLY* 1.3 72.0 - - - -
105A VAL* 1.3 73.8 + - - +
106A LEU* 3.9 5.2 - - - +
142A GLU* 3.4 30.7 - - + +
144A LEU* 4.0 31.2 - - + -
342A TYR* 5.3 1.1 - - - +
344A PRO* 3.6 28.9 - - + +
345A LYS 4.4 2.3 + - - +
346A ALA* 3.4 12.6 - - + -
347A GLU* 2.8 33.5 + - - +
348A GLU 3.4 3.1 + - - -
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Residues in contact with VAL 105 (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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103A GLY 4.1 2.7 - - - +
104A VAL* 1.3 75.4 - - - +
106A LEU* 1.3 61.3 + - - +
107A VAL* 3.6 5.2 + - + -
136A LEU* 4.1 25.1 - - + -
141A ARG* 3.4 51.6 - - + +
142A GLU 2.8 10.6 + - - +
143A VAL* 3.5 10.7 - - + +
144A LEU 3.2 22.2 + - - +
348A GLU* 3.3 22.0 - - + +
350A ILE* 4.1 16.8 - - + -
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Residues in contact with LEU 106 (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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104A VAL* 3.9 2.8 - - + -
105A VAL* 1.3 70.5 - - - +
107A VAL* 1.3 63.2 + - - +
108A GLU* 3.9 0.5 + - - +
144A LEU* 3.4 32.1 - - + +
146A LEU* 4.1 28.9 - - + -
236A LEU* 4.5 10.1 - - + -
312A LYS* 3.6 45.0 + - + +
344A PRO* 3.9 23.1 - - + -
346A ALA* 3.8 14.6 - - + -
348A GLU 2.9 10.0 + - - +
349A THR* 3.3 6.6 - - + -
350A ILE 2.9 25.6 + - - +
351A ASN* 5.3 0.5 + - - -
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Residues in contact with VAL 107 (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 VAL* 4.3 6.7 - - + +
106A LEU* 1.3 77.7 - - - +
108A GLU* 1.3 64.0 + - - +
109A HIS* 4.0 21.3 - - + -
129A GLY 4.0 11.4 - - - +
132A ILE* 4.3 9.6 - - + -
133A ALA* 4.5 5.4 - - + -
136A LEU* 4.5 7.6 - - + -
143A VAL* 4.2 19.7 - - + -
144A LEU 2.8 11.7 + - - +
145A VAL* 3.3 12.0 - - + +
146A LEU 2.8 26.0 + - - +
350A ILE* 3.5 29.2 - - + +
352A VAL* 4.5 6.1 - - + -
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Residues in contact with GLU 108 (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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106A LEU* 3.9 1.9 + - + +
107A VAL* 1.3 72.0 - - - +
109A HIS* 1.3 66.4 + - - +
111A SER* 3.3 26.9 + - - +
146A LEU* 3.3 20.0 - - + +
148A TYR* 3.8 16.1 - - - +
308A PHE* 3.5 12.1 - - - -
312A LYS* 2.7 34.7 + - - +
350A ILE 2.8 10.4 + - - +
351A ASN* 3.6 20.6 - - - +
352A VAL* 3.0 28.1 + - - +
353A VAL* 6.0 1.4 - - - +
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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