Contacts of the strand formed by residues 38 - 44 (chain A) in PDB entry 1I04
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 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A GLU* 3.6 32.3 + - + +
37A TRP* 1.3 79.2 + - - +
39A THR* 1.3 62.9 + - - +
40A ILE* 3.3 3.7 + - + +
60A LEU 3.5 5.6 - - - -
61A GLU* 4.7 11.6 + - - -
138A TYR* 3.0 12.6 - - - -
139A GLY 2.9 44.8 + - - +
140A ARG 3.3 19.5 + - - -
141A GLU* 3.4 13.2 - - - +
142A PRO* 3.9 34.2 - - + +
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Residues in contact with THR 39 (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 HIS* 1.3 73.9 - - - +
40A ILE* 1.3 64.8 + - - +
41A ILE 4.3 3.8 - - - +
42A LEU* 3.6 37.2 - - + -
58A LEU 2.7 24.2 + - - +
59A PHE* 3.9 16.6 - - + +
60A LEU 2.8 20.9 + - - +
138A TYR* 3.4 14.6 - - + -
142A PRO 5.1 0.7 - - - +
169A LEU* 4.1 26.7 - - + +
170A SER* 5.0 0.9 - - - -
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Residues in contact with ILE 40 (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 HIS* 3.6 10.5 - - + +
39A THR* 1.3 78.4 - - - +
41A ILE* 1.3 61.7 + - + +
137A LEU* 2.7 17.6 + - + +
139A GLY* 3.4 21.1 - - - +
141A GLU 3.6 11.9 - - - +
142A PRO 3.4 32.8 - - - +
143A ASP* 3.8 5.6 - - - +
144A LEU* 3.7 20.6 - - + +
149A LYS* 3.7 20.6 - - - -
168A ASP* 3.6 0.3 - - - +
169A LEU 2.7 31.6 + - - -
170A SER* 3.3 25.2 + - - +
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Residues in contact with ILE 41 (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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40A ILE* 1.3 92.8 - - + +
42A LEU* 1.3 73.4 + - - +
136A GLY* 3.6 0.5 - - - -
137A LEU* 2.8 40.7 + - + +
149A LYS* 3.5 40.4 - - + +
152A PHE* 3.7 19.9 - - + -
166A ILE* 3.4 32.1 - - + -
167A ILE 3.3 15.3 - - - +
168A ASP* 4.1 13.7 - - + +
169A LEU* 4.3 0.7 - - - +
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Residues in contact with LEU 42 (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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39A THR* 3.6 17.0 - - + -
41A ILE* 1.3 82.4 - - - +
43A ALA* 1.3 59.8 + - - +
50A ILE* 3.6 21.0 - - + +
56A PHE 3.5 25.6 - - - +
57A ARG* 3.8 6.3 - - - -
58A LEU 3.8 19.5 - - - +
134A LEU* 4.6 8.5 - - + -
135A MET 3.6 3.8 - - - +
136A GLY* 4.0 7.9 - - - -
138A TYR* 3.7 23.6 - - - +
167A ILE* 2.7 36.4 + - + +
169A LEU* 3.8 22.8 - - + +
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Residues in contact with ALA 43 (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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42A LEU* 1.3 76.4 - - - +
44A SER* 1.3 60.3 + - - +
50A ILE* 3.4 3.7 - - - +
134A LEU* 3.3 4.9 - - - +
135A MET* 2.7 37.2 + - + +
152A PHE* 4.4 0.9 - - + -
156A CYS* 3.6 31.4 - - - -
161A ILE* 4.0 6.5 - - + +
165A ASN 3.2 12.8 - - - +
166A ILE* 3.8 13.9 - - + -
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Residues in contact with SER 44 (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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43A ALA* 1.3 77.5 - - - +
45A ASP* 1.3 59.2 + - - +
46A LYS 2.9 29.1 + - - -
47A ARG* 3.7 2.8 + - - -
49A LYS* 4.3 0.6 - - - +
50A ILE* 3.6 21.6 - - - +
132A PHE* 3.3 17.4 - - - -
133A GLN 2.9 17.9 + - - -
134A LEU* 4.4 2.5 - - - -
161A ILE* 3.8 7.8 - - - +
165A ASN* 3.2 28.6 + - - +
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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