Contacts of the strand formed by residues 125 - 137 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A TRP 3.4 7.1 - - - +
69A ASN* 2.9 28.0 + - - +
120A ILE* 3.4 4.7 - - - +
121A PHE* 3.0 42.7 + - + +
123A ASN* 3.0 31.2 + - - +
124A GLY* 1.3 79.6 - - - +
126A VAL* 1.3 61.7 + - - +
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Residues in contact with VAL 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A GLN 4.4 0.2 - - - -
67A LYS* 3.2 27.4 - - - +
68A TRP* 2.8 56.6 + - + +
70A ASP* 4.5 1.3 - - + -
73A LEU* 3.8 25.8 - - + -
93A ILE* 4.5 2.5 - - + -
118A LEU* 3.7 27.1 - - + -
119A ARG 3.5 3.8 - - - +
120A ILE* 4.3 4.0 - - + -
121A PHE* 4.7 2.7 - - - -
124A GLY 3.8 9.9 - - - +
125A ASN* 1.3 80.7 - - - +
127A LEU* 1.3 65.9 + - - +
128A TYR* 4.2 0.7 - - + -
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Residues in contact with LEU 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ARG* 4.1 24.2 - - + -
66A GLN 3.6 3.6 - - - +
67A LYS* 4.0 32.3 - - + -
117A LEU* 3.8 20.2 - - + +
118A LEU* 3.6 5.4 - - - +
119A ARG* 2.8 71.5 + - + +
121A PHE* 4.2 12.7 - - + -
126A VAL* 1.3 72.8 - - - +
128A TYR* 1.3 65.2 + - - +
129A SER* 4.9 1.3 - - - +
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Residues in contact with TYR 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A LEU 3.5 1.7 - - - +
65A ARG* 3.4 1.6 - - - -
66A GLN* 2.9 62.6 + - - +
68A TRP* 3.8 32.5 - + + -
90A LEU* 3.5 35.9 - - + +
95A LYS* 4.0 29.7 - - + +
96A PRO* 5.6 1.8 - - + -
108A PHE* 5.6 0.2 - - - -
116A LYS* 4.4 7.2 - - + -
117A LEU 3.4 10.3 - - - -
118A LEU* 4.9 0.4 - - + +
126A VAL* 4.5 3.1 - - + -
127A LEU* 1.3 76.2 - - - +
129A SER* 1.3 70.7 + - - +
130A ILE* 3.7 32.0 - - + +
112B THR* 5.0 11.5 + - - -
113B THR* 6.2 0.4 - - + +
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Residues in contact with SER 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A PHE* 4.0 9.7 - - - +
64A LEU 3.2 3.9 + - - -
65A ARG* 3.2 35.0 + - - -
116A LYS* 3.3 3.8 - - - +
117A LEU* 2.8 61.3 + - - +
127A LEU* 4.2 2.2 - - - -
128A TYR* 1.3 77.6 - - - +
130A ILE* 1.3 64.2 + - - +
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Residues in contact with ILE 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ILE 3.7 0.2 - - - +
63A PHE* 3.5 3.3 - - - -
64A LEU* 2.8 62.4 + - + +
66A GLN* 5.2 0.4 - - - +
108A PHE* 3.4 36.3 - - + -
115A ASN 3.6 10.1 - - - +
116A LYS* 3.5 25.8 - - + -
128A TYR* 3.7 28.0 - - + +
129A SER* 1.3 77.7 + - - +
131A ARG* 1.3 73.3 + - - +
132A LEU* 3.8 9.7 + - + +
112B THR* 4.9 4.9 - - + -
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Residues in contact with ARG 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ASN* 4.0 10.1 - - - +
61A ASN* 3.1 28.3 + - - +
62A ILE 3.3 11.4 - - - +
63A PHE* 3.8 25.0 - - + -
108A PHE* 4.1 0.2 - - - -
109A HIS* 3.4 47.1 + - + -
111A VAL 5.5 1.8 + - - -
115A ASN* 3.0 48.6 + - + +
130A ILE* 1.3 76.5 - - - +
132A LEU* 1.3 72.5 + - - +
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Residues in contact with LEU 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A VAL 3.8 0.5 - - - +
61A ASN* 3.3 7.3 + - - -
62A ILE* 2.9 42.4 + - + +
64A LEU* 4.2 14.8 - - + -
100A PHE* 3.7 34.8 - - + -
107A ASN 3.6 9.9 - - - +
108A PHE* 3.7 29.2 - - + -
109A HIS* 4.0 1.3 - - - -
130A ILE* 4.1 11.2 - - + +
131A ARG* 1.3 84.0 - - - +
133A THR* 1.3 62.3 + - - +
134A LEU* 4.1 10.5 + - + -
111B VAL* 3.9 19.3 - - + -
112B THR* 4.1 9.6 - - + -
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Residues in contact with THR 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A ARG* 3.8 28.0 - - + -
60A VAL 3.3 7.4 - - - +
61A ASN* 2.9 12.9 + - + +
106A ALA* 3.2 5.2 - - - -
107A ASN* 3.0 48.7 + - - +
109A HIS* 2.7 29.8 + - - -
132A LEU* 1.3 72.5 - - - +
134A LEU* 1.3 67.4 + - - +
135A THR* 5.6 0.9 - - - +
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Residues in contact with LEU 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A TYR 3.7 0.5 - - - +
59A ARG* 3.2 7.1 - - - +
60A VAL* 2.9 48.9 + - + +
62A ILE* 4.0 14.4 - - + -
100A PHE* 3.6 55.9 - - + -
103A GLU* 4.5 3.1 - - + -
105A GLY 3.4 2.5 - - - +
106A ALA* 3.5 27.1 - - + -
132A LEU* 4.4 13.9 - - + -
133A THR* 1.3 80.2 - - - +
135A THR* 1.3 62.1 + - - +
136A LEU* 3.9 16.9 + - + -
154A MET* 4.7 1.3 - - - -
111B VAL* 4.6 1.8 - - + -
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Residues in contact with THR 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A ASP* 3.9 28.0 - - + +
58A TYR 3.3 11.7 - - - +
59A ARG* 4.2 18.6 + - + +
103A GLU* 3.5 2.3 - - - -
104A LYS* 2.7 41.9 + - + -
105A GLY* 2.7 25.1 + - - +
133A THR* 5.6 0.7 - - - +
134A LEU* 1.3 72.6 + - - +
136A LEU* 1.3 56.5 + - - +
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Residues in contact with LEU 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A ASP* 3.1 4.7 - - - +
58A TYR* 2.9 68.5 + - + +
60A VAL* 4.0 15.3 - - + -
100A PHE* 4.2 9.9 - - + -
102A ASN* 3.4 22.7 - - - +
103A GLU* 3.7 27.8 - - + +
104A LYS* 4.4 0.9 - - - -
134A LEU* 4.0 15.0 - - + +
135A THR* 1.3 76.6 - - - +
137A SER* 1.3 62.8 + - - +
154A MET* 3.8 30.7 - - + -
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Residues in contact with SER 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A MET 3.8 8.5 - - - -
58A TYR* 4.3 2.6 - - - -
102A ASN* 2.9 44.5 + - - +
104A LYS* 3.9 22.1 - - - +
136A LEU* 1.3 72.2 - - - +
138A CYS* 1.3 59.6 + - - +
139A PRO* 3.8 12.7 - - - +
153A 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