Contacts of the strand formed by residues 111 - 117 (chain A) in PDB entry 4IE3
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 TYR 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A SER* 3.4 28.9 - - - -
26A VAL 3.6 17.7 - - - -
27A ALA* 3.7 21.8 - - + +
64A HIS* 4.4 2.9 - - + -
65A LEU 4.8 1.1 + - - -
66A LYS* 3.6 47.5 - - + +
106A ALA* 3.0 24.2 + - + +
107A VAL* 3.6 24.1 - - - +
109A ASP* 4.0 25.6 - - + -
110A GLY* 1.3 79.5 - - - +
112A SER* 1.3 62.3 + - - +
113A CYS 3.6 1.4 + - - -
290A SER* 4.1 1.2 + - - +
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Residues in contact with SER 112 (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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25A SER 2.9 16.4 + - - -
26A VAL* 3.2 4.9 - - - +
27A ALA 2.7 29.8 + - - +
110A GLY 3.8 1.2 + - - -
111A TYR* 1.3 71.4 - - - +
113A CYS* 1.3 56.0 + - - +
114A VAL 3.8 0.2 + - - -
289A LEU 3.2 19.6 + - - -
290A SER* 3.1 14.1 + - - -
323A PHE* 3.7 29.4 - - - -
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Residues in contact with CYS 113 (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 ALA* 3.7 8.1 - - - -
29A ILE* 4.4 7.2 - - + -
103A VAL* 3.7 20.0 - - + -
106A ALA* 3.4 33.2 - - - -
107A VAL* 3.6 26.5 - - + -
111A TYR 3.6 0.6 + - - -
112A SER* 1.3 72.0 - - - +
114A VAL* 1.3 58.5 + - - +
115A THR* 3.8 5.9 + - - +
290A SER 2.9 8.9 + - - -
291A ALA* 3.2 9.8 - - + +
292A LEU 2.8 32.2 + - - +
323A PHE* 5.5 0.2 - - - -
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Residues in contact with VAL 114 (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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26A VAL* 3.8 14.8 - - + -
27A ALA 2.7 14.5 + - - +
28A VAL* 3.4 10.7 - - + +
29A ILE* 2.8 27.4 + - - +
54A LEU* 4.8 1.6 - - + -
58A LEU* 4.9 1.3 - - + -
113A CYS* 1.3 71.6 - - - +
115A THR* 1.3 62.6 + - - +
116A LEU* 3.8 26.0 + - + -
292A LEU* 3.4 15.7 - - + +
319A ILE* 4.2 19.7 - - + -
323A PHE* 3.5 37.5 - - + -
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Residues in contact with THR 115 (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 ILE* 3.3 16.7 - - + +
31A ALA* 3.8 24.2 - - + -
99A LEU* 4.4 7.0 - - + -
103A VAL* 4.1 13.2 - - - +
113A CYS* 3.8 4.6 + - - +
114A VAL* 1.3 76.6 + - - +
116A LEU* 1.3 65.0 + - - +
117A GLY 4.0 0.2 + - - -
122A LEU* 3.9 8.7 - - + -
126A THR* 3.5 33.0 - - + +
292A LEU 2.8 9.9 + - - -
293A ASP* 3.4 9.5 + - - +
294A LEU 3.0 26.7 + - - +
295A VAL* 5.1 0.5 - - - +
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Residues in contact with LEU 116 (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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28A VAL* 4.0 15.9 - - + -
29A ILE 2.8 15.7 + - - +
30A GLY* 4.4 0.7 - - - -
31A ALA* 2.8 31.2 + - - +
46A PRO* 3.4 37.6 - - + +
49A ILE* 4.0 17.7 - - + -
50A ARG* 4.2 15.3 - - + +
54A LEU* 3.9 20.2 - - + -
114A VAL* 3.8 13.9 - - + -
115A THR* 1.3 75.5 - - - +
117A GLY* 1.3 59.7 + - - +
294A LEU* 3.8 4.0 - - + -
319A ILE* 3.7 30.1 - - + -
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Residues in contact with GLY 117 (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 ALA 3.7 0.4 - - - -
42A VAL* 4.9 0.4 - - - -
45A GLY* 3.3 12.1 - - - -
46A PRO* 3.2 21.8 - - - +
49A ILE* 4.5 4.2 - - - +
115A THR 4.0 1.0 + - - -
116A LEU* 1.3 74.5 - - - +
118A GLY* 1.3 69.7 + - - -
122A LEU* 3.6 12.5 - - - +
294A LEU 2.9 18.8 + - - +
295A VAL* 4.3 1.5 - - - +
296A GLU 4.6 2.5 - - - -
297A VAL 4.4 3.5 + - - +
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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