Contacts of the strand formed by residues 131 - 142 (chain D) in PDB entry 6ARQ
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 GLY 131 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A GLN* 4.1 5.8 - - - -
57A GLN* 3.4 12.8 - - - -
67A LEU* 4.6 2.2 - - - -
70A VAL* 4.2 11.9 - - - -
125D PHE 3.6 0.9 - - - +
127D THR* 2.7 48.9 + - - -
129D PRO 3.3 3.6 + - - -
130D GLN* 1.3 77.1 - - - +
132D SER* 1.3 62.7 + - - -
133D ARG* 3.7 0.9 + - - +
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Residues in contact with SER 132 (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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55A GLN* 5.0 0.2 + - - -
57A GLN* 2.8 26.1 + - - +
119A MET* 3.3 32.1 - - - -
121A VAL* 4.7 2.8 - - - +
124D LEU* 4.0 20.2 - - - +
125D PHE 3.4 7.0 + - - -
126D VAL* 4.4 12.6 - - - +
130D GLN 4.1 0.7 + - - +
131D GLY* 1.3 70.0 - - - -
133D ARG* 1.3 69.4 + - - +
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Residues in contact with ARG 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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65A ILE 5.8 1.6 + - - -
67A LEU* 5.8 1.6 - - - +
28D ASP 5.4 7.3 - - - +
29D VAL* 3.3 31.3 + - + +
30D VAL* 5.2 0.4 - - - +
31D VAL* 3.8 22.5 - - + +
51D LEU* 4.7 8.7 - - + -
123D CYS 4.0 0.7 - - - +
124D LEU* 3.6 1.2 - - - -
125D PHE* 2.8 35.5 + - + +
127D THR* 4.6 6.7 - - - +
130D GLN* 3.6 36.1 + - + +
131D GLY 4.3 7.6 - - - +
132D SER* 1.3 81.4 + - - +
134D SER* 1.4 61.2 + - - +
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Residues in contact with SER 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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31D VAL* 4.3 4.8 - - - +
122D THR* 4.0 16.6 - - - +
123D CYS 3.3 13.5 - - - -
124D LEU* 3.7 22.2 - - - +
133D ARG* 1.4 77.4 - - - +
135D VAL* 1.3 68.8 + - - +
136D ASP* 6.1 0.3 - - - -
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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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31D VAL* 3.5 43.1 - - + +
33D ALA* 3.7 31.0 - - + +
49D CYS* 3.9 12.1 - - - -
121D TYR 3.9 0.3 - - - +
122D THR* 3.4 6.3 - - - +
123D CYS* 3.1 26.6 + - + +
134D SER* 1.3 78.3 - - - +
136D ASP* 1.3 67.2 + - - +
137D ILE* 4.1 7.5 + - + +
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Residues in contact with ASP 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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1C NAG 3.8 31.5 - - - +
2C FUC 4.6 6.2 - - - +
34D PRO 4.4 0.3 - - - +
35D THR* 3.9 16.1 - - - +
69D HIS* 3.5 8.5 + - - -
120D ASN* 3.8 14.8 - - - +
121D TYR 3.4 3.4 - - - -
122D THR* 3.3 28.0 + - - +
134D SER* 5.8 0.6 - - - -
135D VAL* 1.3 74.8 - - - +
137D ILE* 1.3 61.4 + - - +
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Residues in contact with ILE 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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33D ALA* 4.0 14.8 - - + -
34D PRO* 3.4 24.2 - - + +
35D THR 3.6 3.6 - - - +
37D VAL* 3.8 32.5 - - + -
47D LEU* 4.3 11.2 - - + -
48D PRO* 3.8 17.3 - - + +
49D CYS* 4.5 0.2 - - + -
66D TRP* 3.6 33.0 - - + -
120D ASN* 3.7 2.6 - - - -
121D TYR* 2.8 45.4 + - + +
123D CYS* 4.2 4.5 - - + -
135D VAL* 4.1 13.7 - - + +
136D ASP* 1.3 75.4 - - - +
138D TRP* 1.3 61.8 + - - +
139D LEU 3.9 0.9 + - - -
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Residues in contact with TRP 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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1C NAG 3.5 51.3 - - + +
35D THR 2.8 18.1 + - - +
36D GLN* 3.2 14.4 - - + +
37D VAL* 3.0 27.4 + - - +
118D GLU* 4.0 21.3 + - + -
119D GLY* 3.5 26.7 - - - -
120D ASN* 3.5 26.7 - - + +
136D ASP 4.3 0.2 - - - -
137D ILE* 1.3 73.7 - - - +
139D LEU* 1.3 75.3 + - - +
140D ARG* 3.8 22.6 + - + +
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Residues in contact with LEU 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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37D VAL* 3.7 26.9 - - + +
39D GLY 4.8 2.7 - - - +
45D VAL* 3.7 26.7 - - + -
47D LEU* 4.3 7.4 - - + -
110D MET* 3.8 25.8 - - + -
113D LEU* 3.9 23.8 - - + -
117D ASP* 3.4 23.1 - - + +
118D GLU* 3.3 21.8 - - - +
119D GLY 2.8 14.5 + - - +
121D TYR* 3.7 19.5 - - + -
137D ILE 3.9 1.2 + - - -
138D TRP* 1.3 76.4 + - - +
140D ARG* 1.3 59.8 + - - +
141D VAL* 4.7 3.4 - - + -
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Residues in contact with ARG 140 (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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36D GLN* 5.4 9.0 - - + +
37D VAL 3.2 15.8 + - - +
38D PRO* 3.7 6.8 - - + +
39D GLY* 2.9 30.7 + - - +
118D GLU* 3.4 18.5 + - - +
138D TRP* 3.8 22.3 + - + +
139D LEU* 1.3 72.7 - - - +
141D VAL* 1.3 61.3 + - - +
142D LEU* 3.5 28.0 + - + +
173D PRO* 3.6 31.2 - - - +
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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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39D GLY 3.3 3.1 - - - +
41D LEU* 3.8 42.2 - - + +
113D LEU* 3.9 22.2 - - + -
114D ARG 3.4 20.4 - - - +
115D VAL* 4.8 0.7 - - - -
117D ASP 4.3 1.6 - - - -
118D GLU* 3.1 41.1 + - + +
139D LEU* 4.7 2.0 - - + -
140D ARG* 1.3 70.9 + - - +
142D LEU* 1.3 65.0 + - - +
172D ARG* 3.1 32.7 + - - +
173D PRO* 5.1 0.7 - - - +
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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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38D PRO* 3.7 29.4 - - + -
39D GLY 2.8 12.3 + - - +
40D PHE* 3.5 27.9 - - + -
41D LEU* 2.9 32.0 + - - +
140D ARG* 3.8 28.3 - - + +
141D VAL* 1.3 74.2 - - - +
143D ALA* 1.3 60.0 + - - +
172D ARG* 3.3 18.8 - - - +
173D PRO* 3.7 15.9 - - + -
225D HIS* 4.6 3.6 - - + -
226D GLU* 4.4 24.0 - - + -
227D SER* 4.8 6.1 - - - +
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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