Contacts of the strand formed by residues 134 - 145 (chain D) in PDB entry 5IXG
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 GLU 134 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9D TYR* 2.5 31.8 + - + -
46D ARG* 3.7 13.2 + - - -
125D CYS* 3.5 28.8 - - + +
126D MET* 3.5 15.2 - - - +
127D PRO* 4.4 3.6 - - + -
133D ARG* 1.3 75.3 - - - +
135D VAL* 1.3 62.7 + - - +
136D CYS* 4.1 1.1 - - - -
172D VAL* 3.4 3.5 - - - +
173D LYS* 2.7 64.8 + - + +
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Residues in contact with VAL 135 (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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28C LEU* 4.0 14.8 - - + +
124D LYS 4.0 0.3 - - - +
125D CYS* 3.2 2.6 - - - +
126D MET* 2.9 55.9 + - + +
128D HIS* 4.0 26.9 - - + +
134D GLU* 1.3 76.2 - - - +
136D CYS* 1.3 71.1 + - - +
170D GLU* 4.1 19.7 - - + +
171D ALA 3.3 19.7 - - - +
172D VAL* 4.4 12.3 - - + -
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Residues in contact with CYS 136 (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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28C LEU* 4.1 1.8 - - - -
9D TYR* 3.6 29.8 - - + -
44D LEU* 4.6 3.1 - - - -
46D ARG* 4.5 0.9 - - - -
123D PHE* 4.2 7.4 - - + -
124D LYS 3.2 4.7 - - - +
125D CYS* 2.1 44.0 - - - -
134D GLU* 3.9 4.7 - - - -
135D VAL* 1.3 74.7 - - - +
137D GLY* 1.3 58.9 + - - +
170D GLU* 3.3 2.4 - - - -
171D ALA 2.9 34.8 + - - +
201D OTP 3.6 24.2 - - + +
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Residues in contact with GLY 137 (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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27C GLY 5.2 0.2 - - - +
28C LEU* 3.2 30.2 - - - +
122D SER* 4.3 0.3 + - - -
123D PHE* 3.3 4.5 + - - -
124D LYS* 2.7 36.2 + - - +
136D CYS* 1.3 75.0 - - - +
138D VAL* 1.3 64.0 + - - +
169D ALA 3.2 9.4 - - - -
170D GLU* 4.2 2.7 - - - -
201D OTP 4.4 0.2 - - - -
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Residues in contact with VAL 138 (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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28C LEU 3.6 4.2 + - - -
29C SER* 4.2 6.2 - - - -
120D ILE* 4.4 11.2 - - + -
122D SER* 3.2 12.3 - - - +
123D PHE* 3.6 24.5 - - + -
137D GLY* 1.3 79.9 - - - +
139D ASP* 1.3 65.8 + - - +
140D ALA* 4.8 1.3 - - + +
167D ILE* 3.8 3.9 - - + +
168D THR* 3.8 2.6 - - - -
169D ALA* 2.9 47.8 + - + +
201D OTP 3.8 45.3 - - + -
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Residues in contact with ASP 139 (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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29C SER* 5.7 0.4 - - - -
30C VAL* 3.8 23.7 + - + +
32C ARG* 2.7 45.7 + - - -
120D ILE* 3.7 1.0 - - - -
121D ASP* 2.8 40.8 + - + +
122D SER* 3.1 27.8 + - - +
138D VAL* 1.3 75.0 - - - +
140D ALA* 1.3 59.0 + - - +
141D VAL* 5.3 3.3 - - - +
167D ILE 3.1 7.7 - - - +
168D THR* 4.2 2.3 + - - -
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Residues in contact with ALA 140 (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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118D LEU* 4.4 7.0 - - + -
119D LYS 3.2 17.7 - - - +
120D ILE* 4.3 3.8 - - + -
121D ASP 4.3 0.9 - - - +
138D VAL* 4.2 1.8 - - + -
139D ASP* 1.3 76.2 - - - +
141D VAL* 1.3 70.6 + - - +
166D LEU* 3.5 1.2 - - - +
167D ILE* 2.8 41.6 + - + -
201D OTP 3.8 29.4 - - + -
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Residues in contact with VAL 141 (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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32C ARG* 6.1 0.7 - - - +
117D THR 4.1 0.3 - - - +
118D LEU* 3.3 7.4 - - - -
119D LYS* 2.8 69.9 + - + +
121D ASP* 3.7 17.3 - - - +
139D ASP* 5.3 5.4 - - - +
140D ALA* 1.3 80.7 - - - +
142D GLY* 1.3 61.1 + - - +
143D GLU* 6.3 0.2 - - + -
165D LEU 3.2 10.5 - - - +
166D LEU* 4.9 12.1 - - + -
167D ILE* 5.3 0.2 - - - -
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Residues in contact with GLY 142 (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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116D LEU* 4.7 0.9 - - - -
117D THR 3.9 14.6 - - - -
118D LEU* 4.1 10.0 - - - +
141D VAL* 1.3 77.2 - - - +
143D GLU* 1.3 70.8 + - - +
164D LYS* 3.6 1.0 - - - +
165D LEU* 2.8 37.5 + - - +
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Residues in contact with GLU 143 (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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119A LYS* 4.6 13.0 - - - +
116D LEU* 3.7 14.1 - - - +
117D THR 4.9 0.4 + - - -
141D VAL* 6.3 0.4 - - + -
142D GLY* 1.3 79.6 - - - +
144D PHE* 1.3 69.1 + - - +
162D LYS* 3.6 26.9 + - + +
163D THR 3.2 9.2 - - - +
164D LYS* 3.7 35.6 - - + +
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Residues in contact with PHE 144 (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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107D LEU* 4.4 9.0 - - + -
109D LEU* 3.8 30.7 - - + -
115D PRO 6.2 0.4 - - - +
116D LEU* 4.6 9.6 - - + -
143D GLU* 1.3 79.9 - - - +
145D SER* 1.3 65.9 + - - +
146D ARG* 3.9 20.2 - - + -
148D ASP* 5.9 0.4 - - - +
149D PHE* 3.4 29.6 - + + -
161D MET 3.5 0.3 - - - +
162D LYS* 3.6 2.6 - - - -
163D THR* 2.8 55.2 + - + +
165D LEU* 3.8 37.7 - - + -
201D OTP 4.1 10.8 - - + -
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Residues in contact with SER 145 (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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96A ASP* 5.1 2.8 + - - -
144D PHE* 1.3 78.4 - - - +
146D ARG* 1.3 58.5 + - - +
147D ASP* 2.6 22.6 + - - -
148D ASP* 2.9 42.2 + - - +
149D PHE* 4.0 0.2 - - - -
161D MET* 3.3 19.0 - - - +
162D LYS* 4.4 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