Contacts of the strand formed by residues 126 - 138 (chain A) in PDB entry 6HUP
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 THR 126 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A SER* 4.0 14.6 - - - +
70A TRP 3.3 13.5 - - - +
71A LYS* 4.3 12.9 - - + +
120A ARG 3.8 1.2 - - - +
122A THR* 3.2 38.4 + - + +
124A ASP* 3.3 19.4 + - - -
125A GLY* 1.3 74.1 - - - +
127A LEU* 1.3 62.5 + - - +
128A LEU* 5.3 0.3 - - - +
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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
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69A SER* 2.8 31.0 + - - -
70A TRP* 2.8 55.8 + - + +
72A ASP* 4.4 4.7 - - + +
75A LEU* 3.8 28.9 - - + -
94A ILE* 4.2 12.1 - - + -
119A LEU* 4.5 11.9 - - + -
120A ARG 3.5 2.2 - - - +
121A ILE* 3.6 36.8 - - + -
125A GLY 4.2 8.1 - - - +
126A THR* 1.3 73.6 - - - +
128A LEU* 1.3 61.0 + - - +
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Residues in contact with LEU 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ARG* 4.8 9.0 - - + -
68A GLN 3.3 20.0 - - - +
69A SER* 4.3 9.0 - - - -
118A LEU* 3.2 9.9 - - + +
119A LEU* 3.4 3.8 - - - +
120A ARG* 2.9 59.8 + - + +
126A THR 5.3 0.4 - - - +
127A LEU* 1.3 74.9 - - - +
129A TYR* 1.3 62.1 + - - +
130A THR* 4.0 15.0 - - + -
202B THR* 4.2 25.4 - - + -
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Residues in contact with TYR 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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66A PHE 3.6 3.1 - - - +
68A GLN* 2.8 43.9 + - - +
70A TRP* 3.8 24.0 - + + -
91A ALA* 3.6 33.7 + - + +
96A THR* 3.5 32.9 - - + +
117A LYS* 3.3 42.6 + - + +
118A LEU 3.3 11.0 - - - -
119A LEU* 4.1 10.1 - - + -
127A LEU 4.3 0.2 - - - -
128A LEU* 1.3 74.4 - - - +
130A THR* 1.3 59.7 + - - +
131A MET* 3.9 24.3 - - + +
110E THR 5.5 0.3 + - - -
111E VAL* 5.9 1.4 - - - +
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Residues in contact with THR 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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66A PHE 3.3 10.3 - - - -
67A ARG* 3.6 27.1 - - + +
117A LYS* 3.4 4.9 - - - +
118A LEU* 3.2 44.2 + - + +
128A LEU* 4.0 23.1 - - + -
129A TYR* 1.3 77.8 - - - +
131A MET* 1.3 61.9 + - - +
157B TYR* 2.7 17.3 + - - -
202B THR* 4.8 0.9 - - + -
501B ABU 3.3 19.1 + - - +
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Residues in contact with MET 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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65A PHE* 3.2 4.0 - - - -
66A PHE* 2.7 62.7 + - + +
68A GLN* 4.8 4.5 - - - +
109A ALA* 5.7 2.2 - - + -
116A ASN 3.5 4.5 - - - +
117A LYS* 3.7 33.9 - - + -
129A TYR* 3.9 28.9 - - + -
130A THR* 1.3 75.6 - - - +
132A ARG* 1.3 57.9 + - - +
133A LEU* 4.1 17.5 - - + -
157B TYR* 2.9 14.9 + - - -
110E THR* 3.7 36.3 - - + +
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Residues in contact with ARG 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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63A ASP* 3.6 22.2 + - - +
64A VAL 3.6 3.4 - - - -
65A PHE* 3.2 33.0 - - + -
109A ALA* 4.0 0.9 - - - +
110A HIS* 3.4 47.8 + - - +
112A MET 5.0 0.8 + - - -
116A ASN* 3.5 30.0 + - + +
131A MET* 1.3 76.2 - - - +
133A LEU* 1.3 60.3 + - - +
97B TYR* 3.2 36.3 - - - +
98B PHE 2.4 27.9 + - - +
99B LEU* 3.4 23.3 + - - +
101B ASP* 4.0 12.3 + - - +
157B TYR* 4.0 2.2 - - + -
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Residues in contact with LEU 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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63A ASP* 2.9 22.2 - - - +
64A VAL* 2.9 30.0 + - + +
66A PHE* 3.8 20.2 - - + -
101A PHE* 3.6 31.0 - - + -
108A VAL 3.7 1.6 - - - -
109A ALA* 3.8 27.1 - - + -
110A HIS* 4.3 1.8 - - - -
131A MET* 4.2 20.0 - - + -
132A ARG* 1.3 77.9 - - - +
134A THR* 1.3 60.5 + - - +
135A VAL* 4.1 8.3 - - + -
109E VAL* 3.8 21.1 - - + -
110E THR* 3.8 11.4 - - + -
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Residues in contact with THR 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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61A THR* 3.8 26.7 - - + -
62A ILE 3.3 6.5 - - - +
63A ASP* 3.8 12.4 + - + +
106A LYS 4.7 0.6 - - - +
107A SER* 3.3 4.2 - - - -
108A VAL* 2.9 42.7 + - + +
110A HIS* 2.7 31.3 + - + -
133A LEU* 1.3 73.5 + - - +
135A VAL* 1.3 63.0 + - - +
136A ARG* 3.9 2.4 + - + +
101B ASP 5.3 0.3 + - - -
102B LYS* 5.8 1.7 - - - +
109E VAL* 5.2 0.2 - - - +
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Residues in contact with VAL 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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61A THR* 4.6 0.2 - - - -
62A ILE* 2.7 44.7 + - + +
64A VAL* 4.8 6.7 - - + -
101A PHE* 3.7 47.1 - - + -
104A GLY* 4.3 7.4 - - - +
107A SER* 3.8 9.4 - - - -
133A LEU* 4.2 12.8 - - + -
134A THR* 1.3 75.2 - - - +
136A ARG* 1.3 59.7 + - - +
137A ALA* 3.1 26.9 + - + +
155A LEU* 4.0 13.7 - - + -
109E VAL* 4.8 0.2 - - + -
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Residues in contact with ARG 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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59A GLU* 3.1 38.4 + - - +
60A TYR 3.2 8.1 - - - +
61A THR* 4.2 14.4 - - + +
105A LYS* 2.9 45.8 + - - +
106A LYS* 3.4 46.4 - - - +
107A SER* 4.1 5.5 - - - -
134A THR* 3.9 5.1 + - + +
135A VAL* 1.3 69.0 - - - +
137A ALA* 1.3 62.3 + - - +
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Residues in contact with ALA 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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59A GLU* 3.3 6.9 - - - +
60A TYR* 2.7 66.5 + - + +
103A ASN* 3.3 20.0 - - - +
104A GLY* 4.2 1.8 - - - -
135A VAL* 3.1 17.6 + - + +
136A ARG* 1.3 76.3 - - - +
138A GLU* 1.3 61.0 + - - +
155A LEU* 4.2 3.6 - - + -
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Residues in contact with GLU 138 (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 MET* 4.1 8.5 - - + +
60A TYR* 4.6 1.3 - - - -
103A ASN* 2.7 46.3 + - + +
104A GLY 5.6 0.3 - - - +
105A LYS* 3.9 30.0 - - + +
137A ALA* 1.3 72.7 - - - +
139A CYS* 1.3 59.5 + - - +
140A PRO* 3.4 21.1 - - + +
154A PRO* 4.3 0.9 - - - +
156A LYS* 5.3 0.2 + - - -
46E SER* 3.9 30.0 + - - -
48E ASP* 4.2 3.5 - - - +
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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