Contacts of the helix formed by residues 157 - 169 (chain B) in PDB entry 6NCM
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 157 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155B PRO* 3.1 6.5 - - - +
156B THR* 1.3 77.8 + - - +
158B TRP* 1.3 62.1 + - - +
159B LYS 3.3 1.3 - - - -
160B ASN* 3.1 26.2 + - - +
161B SER* 3.3 16.5 + - - -
15D T 4.6 1.1 + - - -
16D A 5.4 7.9 - - - -
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Residues in contact with TRP 158 (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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119B PHE* 4.1 10.3 - + + -
141B TYR* 4.0 21.5 - + + -
144B ILE* 3.7 27.6 - - + -
145B LEU* 3.8 36.6 - - + -
151B PHE* 3.6 48.9 + + + -
154B ALA* 4.8 5.2 - - + -
155B PRO 3.1 25.6 + - - +
156B THR* 3.2 8.9 + - - +
157B GLY* 1.3 77.5 - - - +
159B LYS* 1.3 99.5 + - + +
161B SER* 3.4 10.0 + - - +
162B VAL* 3.3 29.2 + - + +
15D T 5.1 2.0 - - - -
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Residues in contact with LYS 159 (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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141B TYR* 3.3 59.2 + - + +
145B LEU* 5.4 4.4 - - - +
156B THR 3.9 4.9 + - - +
157B GLY 3.3 0.6 - - - -
158B TRP* 1.3 116.2 - - + +
160B ASN* 1.3 67.1 + - - +
162B VAL* 3.3 17.1 - - - +
163B ARG* 3.4 8.6 - - - +
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Residues in contact with ASN 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B THR 4.5 4.6 + - - -
157B GLY* 3.1 21.5 + - - +
159B LYS* 1.3 80.8 - - - +
161B SER* 1.3 62.5 + - - +
163B ARG* 3.1 38.8 + - - +
164B HIS* 3.1 22.5 + - - +
15D T 4.9 1.5 - - - +
16D A 6.0 4.5 - - - +
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Residues in contact with SER 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B PHE* 3.5 24.5 - - - -
157B GLY 3.3 9.5 + - - -
158B TRP 3.4 2.9 + - - -
159B LYS 3.3 0.6 - - - -
160B ASN* 1.3 78.4 - - - +
162B VAL* 1.3 57.6 + - - +
164B HIS* 3.6 2.4 + - - +
165B ASN* 3.2 24.3 + - - +
14D C 3.9 10.3 + - - +
15D T 2.4 54.3 + - - +
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Residues in contact with VAL 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B PHE* 3.6 33.0 - - + -
123B ILE* 3.4 23.2 - - + +
137B VAL* 5.1 3.4 - - + -
140B ILE* 5.2 7.6 - - + -
141B TYR* 3.4 25.6 - - + -
144B ILE* 4.4 12.3 - - + -
158B TRP* 3.3 19.3 - - + +
159B LYS 3.3 13.2 - - - +
161B SER* 1.3 75.0 - - - +
163B ARG* 1.3 64.7 + - + +
165B ASN* 4.4 2.0 - - - -
166B LEU* 2.9 29.7 + - + +
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Residues in contact with ARG 163 (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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137B VAL* 3.9 18.8 - - + -
141B TYR* 3.2 28.4 + - + +
159B LYS* 3.4 7.1 + - - +
160B ASN* 3.1 53.6 + - - +
162B VAL* 1.3 76.7 - - - +
164B HIS* 1.3 60.0 + - - +
166B LEU* 3.2 8.6 + - - +
167B SER* 3.0 30.8 + - - -
189B TRP* 6.0 0.2 - - - -
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Residues in contact with HIS 164 (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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160A ASN* 6.0 0.2 - - - -
160B ASN 3.1 12.7 + - - +
161B SER 3.8 2.0 - - - +
162B VAL 3.4 0.2 - - - -
163B ARG* 1.3 77.2 - - - +
165B ASN* 1.3 61.9 + - - +
167B SER* 4.7 0.7 - - - -
168B LEU* 3.2 61.5 + - + +
1C A 3.8 15.9 - - - +
2C T 2.7 32.0 + - - +
3C A 3.8 2.5 + - - -
14D C 3.7 24.4 - + - -
15D T 3.1 42.5 + - + +
16D A 3.8 2.5 - - - +
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Residues in contact with ASN 165 (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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119B PHE* 3.7 2.2 - - + -
120B SER* 2.6 43.8 + - - +
123B ILE* 4.2 7.2 - - + -
161B SER 3.2 15.0 + - - +
162B VAL* 3.8 5.6 - - - +
164B HIS* 1.3 79.6 + - - +
166B LEU* 1.3 64.3 + - - +
169B ASN* 3.1 39.3 + - - +
172B PHE* 3.8 5.0 - - - -
13D G 4.0 8.0 + - + +
14D C 2.8 25.0 + - - +
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Residues in contact with LEU 166 (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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123B ILE* 3.9 20.6 - - + +
137B VAL* 4.3 16.8 - - + -
140B ILE* 3.6 18.2 - - + -
162B VAL* 2.9 20.4 + - + +
163B ARG* 3.2 7.6 + - - +
165B ASN* 1.3 76.6 - - - +
167B SER* 1.3 58.0 + - - +
172B PHE* 3.7 28.4 - - + +
189B TRP* 3.3 76.8 - - + +
301B MG 2.9 15.6 - - - -
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Residues in contact with SER 167 (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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163B ARG 3.0 17.0 + - - -
164B HIS* 4.0 2.9 - - - -
165B ASN 3.2 0.2 - - - -
166B LEU* 1.3 75.2 - - - +
168B LEU* 1.3 70.9 + - - +
189B TRP* 4.3 13.4 - - - -
301B MG 2.7 20.0 - - - -
1C A 4.6 16.2 + - - -
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Residues in contact with LEU 168 (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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156A THR* 3.6 25.9 + - - +
164B HIS* 3.2 60.0 + - + +
167B SER* 1.3 89.0 - - - +
169B ASN* 1.3 63.5 + - - +
170B LYS 3.7 0.3 + - - -
1C A 4.5 16.2 - - + +
2C T 3.6 31.6 - - + +
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Residues in contact with ASN 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B SER* 3.9 8.9 + - - -
165B ASN* 3.1 33.1 + - - +
167B SER 3.6 0.2 - - - -
168B LEU* 1.3 78.3 - - - +
170B LYS* 1.3 73.8 + - - +
171B CYS* 3.2 24.2 + - - +
172B PHE* 3.4 31.4 + - + +
173B LYS* 4.8 1.0 - - - -
199B LEU* 4.7 0.8 - - - +
301B MG 2.8 19.9 - - - -
13D G 2.9 27.9 + - - -
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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