Contacts of the strand formed by residues 125 - 137 (chain D) in PDB entry 5TIN
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 ASN 125 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68D TRP 3.4 6.9 - - - +
69D ASN* 2.9 27.8 + - - +
120D ILE* 3.4 4.5 - - - +
121D PHE* 3.0 44.6 + - + +
123D ASN* 3.0 30.4 + - - +
124D GLY* 1.3 80.7 - - - +
126D VAL* 1.3 62.2 + - - +
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Residues in contact with VAL 126 (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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66D GLN 4.4 0.2 - - - -
67D LYS* 3.3 10.0 - - - +
68D TRP* 2.7 75.2 + - + +
70D ASP* 4.5 1.6 - - + -
73D LEU* 3.8 26.5 - - + -
93D ILE* 4.5 1.8 - - + -
118D LEU* 3.7 26.7 - - + -
119D ARG 3.5 3.4 - - - +
120D ILE* 4.3 3.6 - - + -
121D PHE* 4.7 2.7 - - - -
124D GLY 3.8 9.4 - - - +
125D ASN* 1.3 80.7 - - - +
127D LEU* 1.3 65.6 + - - +
128D TYR* 4.2 0.4 - - + -
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Residues in contact with LEU 127 (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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204C THR* 4.1 14.1 - - + -
65D ARG* 4.2 23.8 - - + -
66D GLN 3.6 3.4 - - - +
67D LYS* 4.0 31.2 - - + -
117D LEU* 3.8 17.9 - - + +
118D LEU* 3.6 5.7 - - - +
119D ARG* 2.8 74.1 + - + +
121D PHE* 4.2 13.0 - - + -
126D VAL* 1.3 73.7 - - - +
128D TYR* 1.3 66.1 + - - +
129D SER* 4.9 0.4 - - - +
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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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64D LEU 3.5 1.9 - - - +
65D ARG* 3.4 2.4 - - - -
66D GLN* 2.8 61.2 + - - +
68D TRP* 3.8 32.1 - + + -
90D LEU* 3.5 35.1 - - + +
95D LYS* 4.0 29.8 - - + +
96D PRO* 5.6 2.0 - - + -
108D PHE* 5.6 0.5 - - - -
116D LYS* 4.5 7.6 - - + -
117D LEU 3.4 10.8 - - - -
118D LEU* 5.1 0.2 - - + -
126D VAL* 4.5 2.7 - - + -
127D LEU* 1.3 75.9 - - - +
129D SER* 1.3 70.8 + - - +
130D ILE* 3.7 31.1 - - + +
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Residues in contact with SER 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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159C PHE* 3.7 7.5 - - - -
204C THR* 5.0 2.9 - - - -
63D PHE* 3.9 9.5 - - - +
64D LEU 3.2 4.6 + - - -
65D ARG* 3.2 34.6 + - - -
116D LYS* 3.3 4.2 - - - +
117D LEU* 2.8 60.0 + - - +
127D LEU* 4.2 1.3 - - - -
128D TYR* 1.3 77.0 - - - +
130D ILE* 1.3 63.1 + - - +
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Residues in contact with ILE 130 (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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159C PHE* 4.2 4.0 - - - -
62D ILE 3.7 0.5 - - - +
63D PHE* 3.5 1.4 - - - -
64D LEU* 2.8 61.1 + - + +
66D GLN* 5.3 0.9 - - - +
108D PHE* 3.4 35.9 - - + -
115D ASN 3.7 9.6 - - - +
116D LYS* 3.5 26.5 - - + -
128D TYR* 3.7 26.9 - - + +
129D SER* 1.3 77.3 + - - +
131D ARG* 1.3 74.7 + - - +
132D LEU* 3.8 10.1 + - + +
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Residues in contact with ARG 131 (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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99C PHE* 3.5 19.5 - - - +
100C PHE 3.5 13.1 + - - -
101C ALA 3.6 10.5 + - - -
103C GLU* 3.0 47.7 + - - -
159C PHE* 3.7 10.4 - - + -
46D ASN* 4.0 1.0 - - - +
61D ASN* 3.1 26.5 + - - +
62D ILE 3.3 11.0 - - - +
63D PHE* 3.8 20.5 - - + -
108D PHE* 4.1 0.2 - - - -
109D HIS* 3.4 34.2 + - + -
115D ASN* 3.0 48.6 + - + +
130D ILE* 1.3 76.6 - - - +
132D LEU* 1.3 70.4 + - - +
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Residues in contact with LEU 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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60D VAL 3.8 0.7 - - - +
61D ASN* 3.3 7.3 + - - -
62D ILE* 2.9 43.1 + - + +
64D LEU* 4.2 21.5 - - + -
100D PHE* 3.7 33.9 - - + -
106D ALA* 6.3 0.9 - - + -
107D ASN 3.6 11.9 - - - +
108D PHE* 3.7 32.1 - - + -
109D HIS* 4.0 0.9 - - - -
130D ILE* 4.1 13.7 - - + +
131D ARG* 1.3 84.0 - - - +
133D THR* 1.3 61.5 + - - +
134D LEU* 4.4 12.1 - - + -
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Residues in contact with THR 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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104C LYS* 4.9 4.7 + - - +
59D ARG* 3.9 35.0 - - + +
60D VAL 3.3 9.9 - - - +
61D ASN* 2.9 12.6 + - + -
105D GLY 4.5 0.2 - - - -
106D ALA* 3.2 5.2 - - - -
107D ASN* 3.0 48.7 + - - +
109D HIS* 2.7 28.9 + - - -
132D LEU* 1.3 72.7 - - - +
134D LEU* 1.3 66.3 + - - +
135D THR* 5.6 0.7 - - - +
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Residues in contact with LEU 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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58D TYR 3.7 0.5 - - - +
59D ARG* 3.2 7.3 - - - +
60D VAL* 2.9 47.0 + - + +
62D ILE* 4.0 15.5 - - + -
100D PHE* 3.6 55.6 - - + -
103D GLU* 4.5 3.1 - - + -
105D GLY 3.4 2.7 - - - +
106D ALA* 3.5 26.5 - - + -
132D LEU* 4.4 16.2 - - + +
133D THR* 1.3 80.6 - - - +
135D THR* 1.3 62.0 + - - +
136D LEU* 3.8 17.4 + - + -
154D MET* 4.7 1.1 - - - -
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Residues in contact with THR 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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57D ASP* 3.9 27.8 - - + +
58D TYR 3.3 10.8 - - - +
59D ARG* 3.9 17.5 - - + -
103D GLU* 3.5 3.5 - - - -
104D LYS* 2.7 40.6 + - + -
105D GLY* 2.8 25.2 + - - -
133D THR* 5.6 0.7 - - - +
134D LEU* 1.3 74.0 - - - +
136D LEU* 1.3 55.8 + - - +
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Residues in contact with LEU 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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57D ASP* 3.1 4.9 - - - +
58D TYR* 2.8 70.4 + - + +
60D VAL* 4.0 14.8 - - + -
100D PHE* 4.2 10.3 - - + -
102D ASN* 3.4 22.4 - - - +
103D GLU* 3.8 27.4 - - + +
104D LYS* 4.5 0.7 - - - -
134D LEU* 4.0 14.4 - - + +
135D THR* 1.3 75.4 - - - +
137D SER* 1.3 62.9 + - - +
153D ILE 4.4 0.2 - - - +
154D MET* 3.8 31.0 - - + -
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Residues in contact with SER 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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56D MET 3.8 7.9 - - - -
58D TYR* 4.3 3.1 - - - -
102D ASN* 2.9 44.1 + - - +
104D LYS* 3.9 22.5 - - - +
136D LEU* 1.3 71.8 - - - +
138D CYS* 1.3 59.3 + - - +
139D PRO* 3.8 13.0 - - - +
153D ILE* 4.4 4.7 + - - +
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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