Contacts of the strand formed by residues 28 - 36 (chain A) in PDB entry 1I16
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 ALA 28 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A SER* 3.6 31.0 + - - -
25A THR 3.4 13.5 + - - +
27A GLU* 1.3 74.9 - - - +
29A THR* 1.3 68.5 + - - +
115A ARG* 4.4 16.2 - - - -
116A ARG 3.6 4.3 - - - -
117A LYS* 3.9 15.7 - - + +
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Residues in contact with THR 29 (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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27A GLU 5.1 1.5 + - - -
28A ALA* 1.3 81.0 - - - +
30A VAL* 1.3 68.1 + - - +
31A CYS* 4.3 7.3 - - - -
115A ARG* 3.2 2.7 - - - +
116A ARG* 2.8 40.9 + - - +
121A SER* 5.0 8.8 - - - -
123A GLU 6.0 2.5 - - - +
124A THR* 6.3 3.4 - - + -
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Residues in contact with VAL 30 (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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29A THR* 1.3 73.5 - - - +
31A CYS* 1.3 71.7 + - - +
32A THR* 3.8 20.6 + - - +
83A LEU* 5.6 3.1 - - + -
113A VAL* 4.2 15.9 - - + -
114A ILE 3.0 7.6 - - - +
115A ARG* 3.4 41.1 - - + +
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Residues in contact with CYS 31 (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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29A THR* 4.3 9.4 - - - -
30A VAL* 1.3 84.9 - - - +
32A THR* 1.3 59.9 + - - +
33A VAL* 3.1 20.2 - - + +
77A GLN* 4.1 12.3 - - - +
112A ILE 3.9 0.5 - - - +
114A ILE* 2.6 51.3 + - + +
116A ARG* 5.3 2.5 - - - -
123A GLU* 5.6 7.4 - - - -
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Residues in contact with THR 32 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A VAL* 3.8 14.5 + - - +
31A CYS* 1.3 71.2 - - - +
33A VAL* 1.3 64.7 + - - +
111A THR* 4.2 17.0 - - + -
112A ILE 3.3 14.1 - - - +
113A VAL* 4.0 17.4 - - + +
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Residues in contact with VAL 33 (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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31A CYS* 3.1 23.8 - - + +
32A THR* 1.3 76.3 - - - +
34A THR* 1.3 55.2 + - - +
72A GLN* 3.6 23.8 - - - +
74A GLU 5.4 0.4 - - - +
75A THR* 3.9 21.3 - - + +
77A GLN* 4.3 9.9 - - - +
111A THR* 3.3 4.5 - - - +
112A ILE* 2.4 69.5 + - + +
114A ILE* 5.5 0.2 - - + -
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Residues in contact with THR 34 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A VAL* 1.3 75.9 - - - +
35A LEU* 1.3 69.4 + - - +
69A ALA* 5.8 0.3 - - - -
72A GLN* 3.6 21.8 + - - +
75A THR* 4.0 11.6 + - - +
109A PRO* 3.9 25.3 - - + +
110A VAL 2.8 9.0 - - - +
111A THR* 3.5 29.8 - - + +
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Residues in contact with LEU 35 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A THR* 1.3 72.9 - - - +
36A GLU* 1.3 60.1 + - - +
42A LEU* 4.0 25.4 - - + +
44A PHE* 5.8 2.2 - - + -
68A ALA* 4.6 3.6 - - + -
69A ALA* 4.1 16.4 - - + +
75A THR* 3.0 28.5 - - - +
76A VAL* 3.8 19.5 - - + -
109A PRO* 3.2 7.3 - - - +
110A VAL* 2.4 67.7 + - + +
112A ILE* 2.8 42.8 - - + -
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Residues in contact with GLU 36 (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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35A LEU* 1.3 77.4 - - - +
37A LYS* 1.3 60.5 + - - +
38A MET* 3.0 39.5 + - + +
39A SER* 5.7 0.2 - - - -
42A LEU* 3.8 13.5 - - - -
67A GLY 3.3 4.3 - - - +
68A ALA* 3.0 41.4 - - + +
69A ALA 4.3 2.7 - - - +
71A GLU* 3.2 30.7 - - - +
108A GLY 3.2 7.9 - - - +
109A PRO* 4.7 0.2 - - - -
110A VAL* 3.9 1.8 - - - -
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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