Contacts of the strand formed by residues 145 - 152 (chain D) in PDB entry 1XFB
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 PHE 145 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23D ILE* 3.6 30.5 - - + -
30D ILE* 4.4 7.0 - - + -
76D GLY* 4.3 5.4 - - - -
77D VAL 3.7 22.7 - - - -
78D ILE* 3.6 20.4 - - + -
104D VAL* 3.6 22.0 - - + -
105D VAL 3.2 19.7 - - - -
106D GLY* 2.9 41.8 - - - -
107D ILE* 3.2 8.7 + - - +
143D ALA 3.7 0.2 - - - -
144D ASP* 1.3 82.0 - - - +
146D ALA* 1.3 61.2 + - - +
183D ILE* 3.7 6.0 - - - +
184D VAL* 2.9 21.5 - - + +
186D ILE* 3.6 34.8 - - + -
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Residues in contact with ALA 146 (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 ILE* 3.2 16.8 - - + +
109D VAL* 3.9 17.7 - - + -
135D CYS* 5.7 0.7 - - - -
145D PHE* 1.3 78.8 - - - +
147D LYS* 1.3 63.1 + - - +
174D TYR* 3.2 10.1 - - + +
178D CYS* 4.1 11.4 - - - -
183D ILE* 3.7 14.3 - - + +
184D VAL 2.8 7.3 + - - -
186D ILE* 2.8 31.9 + - - +
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Residues in contact with LYS 147 (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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32D ALA* 5.1 0.8 - - - +
34D ASP* 3.2 32.5 + - - +
78D ILE* 4.0 28.5 - - + -
107D ILE 3.0 5.1 + - - -
108D LYS* 3.4 12.0 - - + +
109D VAL* 3.0 26.7 + - - +
110D ASP* 3.9 2.3 + - - +
146D ALA* 1.3 76.5 - - - +
148D TRP* 1.3 63.0 + - - +
149D ARG* 4.2 16.2 - - - +
174D TYR* 3.3 4.3 - - - -
186D ILE* 4.0 9.2 - - + +
188D GLU* 2.8 29.9 + - + +
230D LYS* 3.0 31.5 - - + +
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Residues in contact with TRP 148 (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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109D VAL* 4.0 2.9 - - + -
110D ASP* 3.6 22.2 - - + -
125D THR* 3.3 37.1 - - + -
126D GLN 3.5 0.4 - - - -
127D GLY* 3.4 28.7 - - - -
128D LEU* 3.4 38.6 - - + -
131D LEU* 4.4 5.2 - - + -
147D LYS* 1.3 75.6 - - - +
149D ARG* 1.3 66.0 + - - +
150D CYS* 3.6 12.0 - - - -
170D VAL* 3.3 25.5 - - + +
171D LEU* 3.6 18.2 - - + +
174D TYR* 3.3 49.9 + + + -
186D ILE 3.7 1.6 + - - -
188D GLU* 3.3 25.1 + - - +
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Residues in contact with ARG 149 (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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108D LYS* 5.7 3.1 - - - +
110D ASP* 3.2 18.1 + - - +
113D VAL* 5.6 1.9 - - - +
125D THR* 2.8 22.0 + - - +
147D LYS* 4.2 11.4 - - - +
148D TRP* 1.3 77.1 - - - +
150D CYS* 1.3 69.9 + - - +
151D VAL* 3.4 31.5 - - + +
188D GLU* 3.3 34.1 - - + +
190D GLU* 2.4 43.6 + - - +
192D LEU* 4.3 7.1 - - - +
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Residues in contact with CYS 150 (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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125D THR* 3.3 9.9 - - - -
148D TRP* 3.6 24.2 + - - -
149D ARG* 1.3 78.3 - - - +
151D VAL* 1.3 65.7 + - - +
152D LEU* 5.6 2.0 - - + -
167D ASN* 3.3 35.7 - - + +
170D VAL* 4.6 2.7 - - - -
171D LEU* 3.6 26.7 - - + -
188D GLU 3.0 13.1 + - - +
189D PRO* 4.5 6.1 - - + -
190D GLU* 3.2 22.1 + - - +
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Residues in contact with VAL 151 (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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113D VAL* 4.7 13.3 - - + +
123D THR* 3.5 30.5 + - - +
124D THR 5.9 0.2 - - - -
125D THR* 4.5 1.4 + - - -
149D ARG* 3.4 39.5 - - + +
150D CYS* 1.3 83.0 - - - +
152D LEU* 1.3 72.7 + - - +
153D LYS* 5.9 0.4 - - + -
167D ASN* 4.2 2.9 + - - +
190D GLU 3.4 3.4 - - - +
192D LEU* 3.5 40.6 - - + -
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Residues in contact with LEU 152 (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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122D GLU* 6.1 0.2 - - - -
123D THR 5.2 0.2 - - - +
150D CYS* 5.6 1.6 - - + -
151D VAL* 1.3 80.6 - - - +
153D LYS* 1.3 61.3 + - - +
159D PRO* 5.0 9.6 - - + -
163D ALA* 3.8 19.3 - - + +
164D ILE* 4.6 13.2 - - + -
167D ASN* 3.5 35.4 - - + +
189D PRO* 5.6 6.1 - - + -
190D GLU 2.8 13.0 + - - +
191D ILE* 4.2 13.0 - - + -
192D LEU* 2.9 31.7 + - - +
209D VAL* 3.3 45.5 - - + -
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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