Contacts of the strand formed by residues 124 - 130 (chain D) in PDB entry 1I3R
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 THR 124 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C PRO* 6.0 3.1 - - + -
122D GLU 4.3 3.6 + - - -
123D PRO* 1.3 74.0 + - - +
125D VAL* 1.3 60.9 + - - +
126D THR* 3.7 12.1 + - - +
144D SER 3.3 11.6 - - - +
146D SER* 2.9 35.1 + - - +
147D ASP* 4.1 12.4 + - - +
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Residues in contact with VAL 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D PRO* 3.8 19.6 + - + +
124D THR* 1.3 75.7 - - - +
126D THR* 1.3 65.9 + - - +
143D CYS* 3.9 18.4 - - - -
144D SER 3.4 4.5 - - - +
145D VAL* 4.5 3.6 - - + -
199D CYS* 4.6 3.6 - - + +
201D VAL* 3.7 37.9 - - + -
210D VAL* 4.3 19.5 - - + -
212D VAL* 3.5 34.2 - - + +
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Residues in contact with THR 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C PRO* 4.9 12.1 - - + +
124D THR* 4.4 12.9 + - - +
125D VAL* 1.3 75.6 + - - +
127D VAL* 1.3 70.3 + - - +
128D TYR* 3.8 22.0 - - + -
142D VAL 3.7 0.2 - - - +
143D CYS* 3.4 4.0 - - - -
144D SER* 2.6 48.6 + - - -
212D VAL* 4.9 2.0 - - - -
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Residues in contact with VAL 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126D THR* 1.3 85.6 - - - +
128D TYR* 1.3 71.6 + - - +
141D LEU* 4.4 4.0 - - + -
142D VAL 3.2 4.0 - - - +
143D CYS* 4.2 6.1 - - - -
157D TRP* 3.7 22.4 - - + -
199D CYS* 3.8 22.7 - - + -
212D VAL* 3.6 36.4 - - + +
213D GLU 5.2 0.2 - - - +
214D TRP* 3.5 39.3 - - + -
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Residues in contact with TYR 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C PRO* 5.5 7.8 - - + +
126D THR* 3.8 17.3 - - + -
127D VAL* 1.3 84.0 - - - +
129D PRO* 1.3 78.2 - - + +
130D THR* 3.9 15.9 - - + -
141D LEU* 4.2 4.3 - - - -
142D VAL* 2.6 67.2 + - + +
144D SER* 4.0 25.7 - - - -
184D LEU* 4.3 9.7 - - - +
214D TRP* 4.5 1.6 - - - +
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Residues in contact with PRO 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182C GLU 5.7 1.2 - - - +
128D TYR* 1.3 92.5 - - + +
130D THR* 1.3 64.9 + - - +
138D HIS* 3.4 35.7 + - + +
140D LEU 3.3 13.2 - - - +
141D LEU* 4.1 10.8 - - + -
191D PRO* 5.5 0.4 - - + -
214D TRP* 3.7 33.7 - - + +
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Residues in contact with THR 130 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182C GLU 5.7 5.6 - - - +
128D TYR* 3.9 22.4 - - + -
129D PRO* 1.3 79.1 - - - +
131D LYS* 1.3 80.2 + - - +
138D HIS* 3.9 14.0 - - - +
139D ASN* 4.1 3.8 + - - +
140D LEU* 3.1 36.3 + - - +
142D VAL* 4.1 10.8 - - + +
186D MET* 5.0 2.8 - - + +
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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