Contacts of the strand formed by residues 132 - 142 (chain D) in PDB entry 4U9W
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 ASP 132 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25D VAL* 3.7 5.6 - - - +
128D VAL* 3.1 6.6 - - - -
129D GLU 2.9 32.7 + - - +
130D CYS* 4.0 8.8 - - - +
131D GLY* 1.3 85.5 - - - +
133D GLU* 1.3 65.1 + - - +
134D VAL* 3.4 12.0 + - + +
169D LYS* 3.5 30.2 - - + +
170D LYS* 4.6 17.8 + - - -
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Residues in contact with GLU 133 (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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25D VAL* 3.4 45.6 - - + +
28D LYS* 4.2 22.4 + - + +
29D VAL* 4.1 4.5 - - + -
127D ASP 3.7 5.6 - - - -
132D ASP* 1.3 72.7 - - - +
134D VAL* 1.3 63.2 + - - +
167D GLN 4.2 7.8 - - - +
168D MET* 3.8 26.7 - - + -
169D LYS* 2.7 72.1 + - - +
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Residues in contact with VAL 134 (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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126D PHE* 3.5 1.6 - - - -
127D ASP* 2.9 45.8 + - + +
129D GLU* 4.0 18.4 - - + -
132D ASP* 3.6 16.6 - - + +
133D GLU* 1.3 81.3 - - - +
135D LEU* 1.3 62.2 + - - +
136D TYR* 4.1 21.3 - - + +
168D MET* 3.5 12.0 - - - +
170D LYS* 3.5 18.8 - - + +
172D MET* 3.3 32.1 - - + -
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Residues in contact with LEU 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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124D PHE* 3.5 47.3 - - + -
125D ARG 3.3 4.9 - - - +
126D PHE* 3.8 21.8 - - + +
134D VAL* 1.3 72.4 - - - +
136D TYR* 1.3 60.8 + - - +
137D CYS 3.7 1.0 + - - +
159D LEU* 3.3 45.5 - - + +
162D MET* 4.3 5.2 - - + -
163D ALA* 3.9 17.5 - - + +
168D MET* 3.9 7.4 - - + +
170D LYS 2.8 15.5 + - - +
171D VAL* 3.2 7.8 - - + -
172D MET 2.8 24.8 + - - -
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Residues in contact with TYR 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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124D PHE* 3.1 4.7 - - - -
125D ARG* 2.8 40.4 + - + +
127D ASP* 5.3 1.1 - - + -
129D GLU* 4.1 9.4 - - + -
134D VAL* 3.7 9.8 - - + -
135D LEU* 1.3 73.2 - - - +
137D CYS* 1.3 76.1 - - - +
138D TYR* 3.5 20.7 + + + -
172D MET* 3.5 38.4 - - + -
173D LEU* 3.7 14.4 - - - -
174D THR* 2.5 24.7 + - - -
213D ILE* 3.9 10.4 - - + +
2H GLY 3.7 19.7 - - - -
3H ARG* 3.8 43.8 - - + +
4H GLY 3.9 2.3 + - - -
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Residues in contact with CYS 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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122D SER* 3.8 1.6 - - - -
123D HIS 3.9 2.5 - - - -
124D PHE* 4.2 2.9 - - - -
135D LEU* 3.7 2.0 + - - +
136D TYR* 1.3 78.1 - - - +
138D TYR* 1.3 63.3 + - - +
139D GLU 3.3 28.5 - - - -
140D VAL* 4.3 4.3 - - - -
156D ILE* 4.1 14.8 - - + -
159D LEU* 3.6 30.1 - - + -
171D VAL* 4.6 7.4 - - + -
172D MET 2.7 15.9 + - - +
173D LEU* 3.5 28.4 - - + +
174D THR 4.4 1.4 + - - -
186D PHE* 5.5 0.4 - - - -
1H SER 5.0 1.7 + - - -
2H GLY 4.4 0.5 - - - +
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Residues in contact with TYR 138 (chain D).
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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100D GLU* 3.7 31.2 - - + -
123D HIS* 2.7 48.6 + + - +
125D ARG* 3.4 45.2 + - + -
136D TYR* 3.7 20.0 - + + -
137D CYS* 1.3 74.5 - - - +
139D GLU* 1.3 60.9 + - + +
1H SER* 3.1 7.4 - - - -
2H GLY 2.8 33.0 + - - +
3H ARG* 2.6 58.3 + - + -
101H NA 4.4 1.1 - - - -
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Residues in contact with GLU 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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77D THR* 3.6 13.7 - - - +
97D LYS* 2.7 37.6 + - - +
100D GLU* 4.2 0.9 - - - +
101D MET* 4.9 5.2 - - + -
121D PHE* 3.8 26.9 - - + -
122D SER* 3.1 23.3 + - - -
123D HIS* 3.1 27.9 + - + +
137D CYS* 3.3 8.8 - - - -
138D TYR* 1.3 89.8 - - + +
140D VAL* 1.3 58.8 + - - +
141D GLN* 3.4 17.1 + - + -
1H SER* 2.8 22.2 + - - -
2H GLY 3.6 0.2 + - - -
101H NA 3.6 4.0 - - - -
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Residues in contact with VAL 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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121D PHE 3.4 9.4 - - - +
122D SER* 4.7 2.7 - - - -
137D CYS* 4.4 2.9 - - - -
139D GLU* 1.3 74.8 - - - +
141D GLN* 1.3 60.4 + - - +
142D LEU* 4.0 12.1 - - + -
152D GLY 4.6 7.4 - - - +
155D LEU* 4.5 11.9 - - + -
156D ILE* 4.1 22.7 - - + -
186D PHE* 3.5 33.0 - - + -
301D COA 2.8 59.3 + - + +
101H NA 3.4 5.8 - - - -
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Residues in contact with GLN 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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76D LEU* 3.6 10.2 - - + +
77D THR* 3.7 13.7 - - - +
80D ASN* 2.8 39.7 + - - +
81D MET* 3.3 32.8 - - - +
120D ALA* 3.2 2.8 - - - -
121D PHE* 2.9 65.7 + - + -
139D GLU* 3.4 17.2 + - + +
140D VAL* 1.3 86.0 + - - +
142D LEU* 1.3 63.4 + - - +
301D COA 3.5 13.4 + - - +
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Residues in contact with LEU 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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76D LEU* 3.8 4.5 - - - -
80D ASN* 3.4 6.7 + - - +
119D VAL 3.6 2.7 - - - -
120D ALA* 3.6 17.9 - - + -
140D VAL* 4.0 20.4 - - + -
141D GLN* 1.3 82.4 - - - +
143D GLU* 1.3 71.4 + - - +
146D VAL* 3.7 25.6 - - + +
147D ARG* 3.1 26.9 + - + -
151D LEU* 4.0 4.9 - - + -
152D GLY* 3.8 18.4 - - - +
155D LEU* 4.2 4.9 - - + -
301D COA 2.8 51.7 + - + +
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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