Contacts of the helix formed by residues 126 - 139 (chain B) in PDB entry 1CF5
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 126 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B LEU* 1.3 78.3 - - - +
127B LEU* 1.3 68.3 + - - -
128B PRO 3.3 2.5 - - - -
129B ALA 3.4 0.5 + - - -
130B LEU* 3.2 20.8 + - - +
155B THR* 4.2 9.7 - - - +
169B VAL* 4.3 7.8 - - - +
172B TYR 3.5 9.2 - - - -
175B THR 4.0 1.3 - - - -
176B ASN* 3.0 7.2 - - - -
177B PHE* 3.6 13.6 - - - -
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Residues in contact with LEU 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B PHE* 4.3 11.4 - - + -
6B LEU* 3.1 24.1 - - + +
9B ALA* 3.6 41.3 - - + +
10B THR 4.4 6.7 - - - +
14B TYR* 3.8 33.2 - - + -
55B TYR* 3.6 6.3 - - + +
126B GLY* 1.3 72.4 - - - -
128B PRO* 1.4 71.1 - - + +
130B LEU* 3.3 8.3 + - + +
131B SER 3.3 4.3 + - - -
169B VAL* 3.8 17.7 - - + +
172B TYR 2.9 8.7 + - - +
173B VAL* 3.7 31.0 - - + +
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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
----------------------------------------------------------
55B TYR* 3.4 20.9 - - + +
127B LEU* 1.4 90.6 - - + +
129B ALA* 1.3 57.7 + - - +
130B LEU 2.9 5.5 + - - -
131B SER* 3.0 15.1 + - - -
132B SER* 3.3 15.7 + - - -
172B TYR 3.4 4.9 - - - +
173B VAL 3.6 7.4 - - - +
174B ALA* 3.8 8.1 - - - +
175B THR* 3.3 34.5 - - - +
176B ASN* 3.4 14.6 - - - +
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Residues in contact with ALA 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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124B ASP* 3.0 33.0 - - + +
125B LEU* 4.0 5.4 - - - -
126B GLY 3.4 0.4 + - - +
127B LEU 3.4 0.2 - - - -
128B PRO* 1.3 76.6 - - - +
130B LEU* 1.3 56.8 + - - +
132B SER* 4.0 9.0 - - - -
133B ALA* 3.3 15.4 + - - +
151B VAL* 3.3 18.7 - - + +
176B ASN* 3.1 25.2 + - - +
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Residues in contact with LEU 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B PHE* 4.5 24.5 - - + -
6B LEU* 4.5 5.8 - - + -
14B TYR* 5.1 4.7 - - + -
17B PHE* 5.8 0.4 - - + -
52B LEU* 5.2 4.5 - - + -
126B GLY 3.2 10.6 + - - +
127B LEU* 3.5 14.4 - - + +
128B PRO 2.9 0.4 + - - -
129B ALA* 1.3 75.5 - - - +
131B SER* 1.3 58.4 + - - +
132B SER 2.8 9.9 + - - -
133B ALA* 2.9 13.9 + - + +
134B ILE* 3.1 32.9 + - + +
151B VAL* 4.3 4.7 - - + +
152B LEU* 4.6 22.2 - - + -
155B THR* 3.1 42.8 - - + +
156B THR* 4.8 6.7 - - + -
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Residues in contact with SER 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LEU* 3.3 26.8 - - - +
54B SER* 2.9 7.3 - - - -
55B TYR* 2.5 55.4 + - - +
127B LEU 3.3 1.6 + - - -
128B PRO 3.0 3.9 + - - -
130B LEU* 1.3 76.0 - - - +
132B SER* 1.3 59.3 + - - +
134B ILE* 4.0 10.3 - - - -
135B THR* 3.2 17.5 + - - -
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Residues in contact with SER 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B TYR* 5.9 1.2 - - - -
128B PRO 3.3 15.2 + - - -
129B ALA* 4.1 8.9 - - - -
130B LEU 2.9 0.6 - - - -
131B SER* 1.3 78.8 + - - +
133B ALA* 1.3 58.4 + - - +
134B ILE 3.1 4.3 - - - -
135B THR* 3.9 5.7 - - - +
136B THR* 2.8 35.8 + - - +
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Residues in contact with ALA 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ALA 3.3 15.4 + - - +
130B LEU* 2.9 11.5 + - + +
132B SER* 1.3 75.0 - - - +
134B ILE* 1.3 57.9 + - + +
137B LEU* 3.0 37.2 + - - +
148B ALA* 3.3 36.9 - - + +
151B VAL* 3.7 11.7 - - + -
152B LEU* 4.4 7.6 - - + +
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Residues in contact with ILE 134 (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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6B LEU* 4.3 7.9 - - + -
52B LEU* 4.1 19.7 - - + +
53B THR 4.0 8.3 - - - +
54B SER* 3.9 23.8 - - - +
58B GLU 3.6 25.1 - - - +
60B ILE* 3.9 27.9 - - + +
130B LEU* 3.3 31.0 - - + +
131B SER* 4.0 8.7 - - - -
133B ALA* 1.3 78.8 - - - +
135B THR* 1.3 57.3 + - - +
137B LEU* 3.6 5.4 - - - +
138B PHE* 2.7 32.6 + - - +
152B LEU* 5.8 1.8 - - + -
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Residues in contact with THR 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B SER* 4.0 0.9 - - - -
56B ALA* 5.8 0.3 - - - +
58B GLU* 2.8 39.0 + - - +
131B SER 3.2 15.8 + - - -
132B SER* 3.6 9.6 + - - -
134B ILE* 1.3 77.8 - - - +
136B THR* 1.3 60.5 + - + +
138B PHE* 3.0 16.8 + - - +
139B TYR* 3.0 34.6 + - + -
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Residues in contact with THR 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B SER* 2.8 20.9 + - - +
133B ALA* 3.7 0.9 + - - -
135B THR* 1.3 76.8 - - + +
137B LEU* 1.3 62.6 + - - +
139B TYR* 3.5 20.4 - - - +
140B TYR* 3.8 5.4 - - - -
141B ASN 4.4 0.3 + - - -
144B SER* 4.0 26.3 + - - -
145B ALA* 4.9 0.9 - - - -
148B ALA* 3.1 27.9 - - + +
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Residues in contact with LEU 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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60B ILE* 4.0 20.4 - - + -
74B TYR* 2.6 46.9 + - + +
76B THR* 3.8 2.1 - - - +
133B ALA 3.0 23.3 + - - +
134B ILE 3.7 4.3 - - - +
135B THR 3.1 0.4 - - - -
136B THR* 1.3 82.1 - - - +
138B PHE* 1.3 66.3 + - - +
139B TYR 3.2 1.8 - - - -
140B TYR 3.8 3.6 + - - -
145B ALA* 4.1 20.2 - - + +
148B ALA* 3.5 24.0 - - + +
149B LEU* 4.0 24.9 - - + -
152B LEU* 4.1 19.5 - - + -
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Residues in contact with PHE 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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58B GLU* 3.6 35.0 - - + -
59B THR 3.3 37.2 - - - -
60B ILE* 3.7 6.3 - - + -
76B THR* 2.6 35.3 + - - +
77B ARG* 3.1 56.1 + - + -
134B ILE 2.7 16.7 + - - +
135B THR 3.0 4.2 + - - +
137B LEU* 1.3 80.8 - - - +
139B TYR* 1.3 74.7 + + - +
140B TYR 3.4 2.8 + - - -
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Residues in contact with TYR 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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58B GLU* 3.7 28.1 + - - +
77B ARG* 3.9 26.9 - - - +
135B THR* 3.0 34.4 + - + +
136B THR* 3.5 11.4 - - - +
138B PHE* 1.3 89.1 - + - +
140B TYR* 1.3 67.2 + - - +
141B ASN* 3.5 5.5 + - - +
144B SER* 5.1 0.5 + - - -
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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