Contacts of the helix formed by residues 125 - 139 (chain B) in PDB entry 3CRK
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 125 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B TRP* 4.2 9.2 - - + -
122B ARG 4.7 2.4 + - - -
123B HIS 3.2 0.6 - - - -
124B ASN* 1.3 90.1 + - - +
126B VAL* 1.3 61.7 + - - +
127B VAL 3.2 2.9 - - - -
128B PRO* 3.3 20.0 - - + +
129B THR* 2.6 40.0 + - - +
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Residues in contact with VAL 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B VAL* 4.4 4.6 - - + +
87B TRP* 3.6 30.3 - - + -
88B TYR* 4.3 7.4 - - + +
123B HIS* 3.2 37.8 + - + +
124B ASN 3.4 1.0 - - - -
125B ASP* 1.3 76.1 - - - +
127B VAL* 1.3 59.2 + - - +
129B THR* 3.9 0.4 - - - -
130B MET* 2.8 29.5 + - - +
158B PHE* 3.5 36.1 - - + -
162B ARG* 3.7 22.8 - - + +
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Residues in contact with VAL 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ASN 5.9 0.7 - - - +
125B ASP* 4.4 0.2 - - - +
126B VAL* 1.3 76.5 - - - +
128B PRO* 1.4 71.7 - - + +
131B ALA* 3.1 20.7 + - + +
159B TYR* 3.3 26.5 + - + +
162B ARG* 3.8 36.5 - - - +
328B TYR* 5.2 4.3 - - + -
332B ILE* 3.5 33.9 - - + -
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Residues in contact with PRO 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ASN 5.0 1.3 - - - +
125B ASP* 3.3 35.4 - - + +
127B VAL* 1.4 98.3 - - + +
129B THR* 1.3 53.5 + - - +
131B ALA* 3.8 6.9 - - + +
132B GLN* 3.0 29.8 + - - +
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Residues in contact with THR 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B SER* 3.1 42.5 - - - +
83B LEU* 4.0 21.0 - - + +
84B VAL* 3.8 11.4 - - + -
87B TRP* 3.6 11.7 - - + -
125B ASP* 2.6 29.9 + - - +
126B VAL 3.9 2.0 - - - -
128B PRO* 1.3 74.5 - - - +
130B MET* 1.3 64.1 + - - +
132B GLN* 3.2 12.0 + - - +
133B GLY 3.1 17.5 + - - -
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Residues in contact with MET 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B ILE* 5.4 2.5 - - + -
71B LEU* 5.4 1.8 - - - -
75B VAL* 5.9 0.7 - - - -
81B VAL* 4.0 31.6 - - + -
84B VAL* 3.9 33.5 - - + +
126B VAL 2.8 21.8 + - - +
129B THR* 1.3 72.0 - - - +
131B ALA* 1.3 60.6 + - - +
133B GLY* 3.2 3.1 + - - +
134B VAL* 3.1 27.5 + - - +
154B PHE* 4.2 15.0 - - + -
155B LEU* 3.6 25.1 - - + -
158B PHE* 3.9 22.4 - - + -
159B TYR* 3.5 20.4 - - + +
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Residues in contact with ALA 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B VAL* 3.1 18.4 + - + +
128B PRO* 3.8 7.4 - - + +
130B MET* 1.3 74.0 - - - +
132B GLN* 1.3 60.6 + - - +
134B VAL* 3.4 3.3 + - - +
135B LEU* 2.9 27.8 + - - +
159B TYR* 3.6 0.6 + - - -
310B THR* 3.8 6.7 - - + +
328B TYR* 3.5 41.7 - - + -
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Residues in contact with GLN 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B SER* 3.6 16.0 + - - +
128B PRO 3.0 16.0 + - - +
129B THR* 3.3 17.7 + - - +
131B ALA* 1.3 76.4 - - - +
133B GLY* 1.3 51.4 + - - +
135B LEU* 3.2 16.1 + - + +
136B GLU* 2.7 48.7 + - + +
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Residues in contact with GLY 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B VAL* 4.9 1.1 - - - +
78B THR* 3.6 17.8 - - - +
80B SER* 3.5 9.8 - - - -
81B VAL* 4.0 8.9 - - - +
129B THR 3.1 10.9 + - - -
130B MET 3.2 5.3 + - - -
132B GLN* 1.3 74.1 - - - +
134B VAL* 1.3 58.8 + - - +
136B GLU* 3.2 19.0 + - - +
137B TYR* 3.0 24.6 + - - +
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Residues in contact with VAL 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B VAL* 4.9 10.1 - - + -
130B MET* 3.1 19.8 + - - +
131B ALA* 3.7 3.4 - - - +
133B GLY* 1.3 75.5 - - - +
135B LEU* 1.3 57.4 + - - +
137B TYR* 3.3 9.0 + - + +
138B LYS* 2.8 26.9 + - + +
151B ILE* 4.5 11.2 - - + -
155B LEU* 3.8 28.3 - - + -
306B TYR 4.8 0.9 - - - +
307B MET* 3.7 28.0 - - - -
310B THR* 3.9 8.1 - - + +
328B TYR* 3.5 22.4 - - - +
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Residues in contact with LEU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B ALA 2.9 13.6 + - - +
132B GLN* 3.3 18.6 - - + +
134B VAL* 1.3 74.1 - - - +
136B GLU* 1.3 58.8 + - + +
137B TYR 3.1 0.4 - - - -
138B LYS* 3.5 3.3 - - + +
139B ASP* 2.9 57.3 + - - +
310B THR* 3.6 21.9 - - + +
311B ALA 3.6 33.9 - - - +
312B PRO* 3.7 7.9 - - + -
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Residues in contact with GLU 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B THR* 3.3 22.2 - - + +
79B PRO* 3.4 17.3 - - + +
80B SER* 3.1 42.3 + - - -
132B GLN* 2.7 31.9 + - + +
133B GLY* 3.2 7.0 + - - +
135B LEU* 1.3 73.6 - - + +
137B TYR* 1.3 56.4 + - - +
139B ASP* 4.8 1.8 - - - +
140B THR* 2.6 31.4 + - - -
141B TYR* 4.8 0.7 - - - -
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Residues in contact with TYR 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B PRO* 5.4 1.1 - - + -
74B ARG* 3.8 30.5 - - + +
75B VAL* 3.7 22.2 - - + -
78B THR* 4.0 4.7 - - + +
133B GLY 3.0 12.6 + - - +
134B VAL* 3.5 12.6 - - - +
135B LEU 3.1 0.4 - - - -
136B GLU* 1.3 76.5 - - - +
138B LYS* 1.3 63.2 + - - +
141B TYR* 2.9 64.3 + + + -
142B GLY 5.6 1.6 - - - -
144B ASP* 4.0 13.2 + - - +
147B SER* 3.2 26.9 + - - -
148B ASN* 4.0 3.8 + - - -
151B ILE* 3.5 28.9 - - + -
307B MET* 3.9 20.4 - - + -
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Residues in contact with LYS 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B VAL 2.8 14.7 + - - +
135B LEU* 3.2 8.0 + - + +
137B TYR* 1.3 80.5 - - - +
139B ASP* 1.3 63.2 + - - +
140B THR 3.2 4.4 + - - -
141B TYR 4.0 3.6 + - - -
142B GLY* 4.0 20.5 + - - +
307B MET* 3.2 50.6 + - + +
308B TYR* 5.3 1.0 - - - +
310B THR* 3.4 39.5 - - - +
312B PRO 4.3 13.2 - - - -
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Residues in contact with ASP 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B LEU* 2.9 28.1 + - + +
136B GLU* 5.3 1.1 - - - -
137B TYR 3.4 0.2 - - - -
138B LYS* 1.3 83.2 - - - +
140B THR* 1.3 64.5 + - - +
312B PRO* 3.2 45.9 - - - +
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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