Contacts of the helix formed by residues 156 - 169 (chain A) 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 THR 156 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154A ALA 4.2 4.3 - - - +
155A PRO* 1.3 72.2 - - + +
157A GLY* 1.3 61.5 + - - +
158A TRP* 3.1 11.2 + - - +
159A LYS* 3.6 15.1 + - - +
160A ASN* 3.4 10.6 + - - +
168B LEU* 3.6 23.5 + - - +
170B LYS* 5.4 9.5 + - + +
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Residues in contact with GLY 157 (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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155A PRO* 2.9 6.8 + - - +
156A THR* 1.3 78.2 + - - +
158A TRP* 1.3 62.9 + - - +
159A LYS 3.3 0.4 - - - -
160A ASN* 3.1 24.7 + - - +
161A SER* 3.2 15.9 + - - -
11D A 5.8 4.5 - - - -
12D C 3.9 19.6 - - - -
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Residues in contact with TRP 158 (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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119A PHE* 3.7 17.9 - + + -
141A TYR* 4.0 25.1 - + + -
144A ILE* 4.5 16.4 - - + -
145A LEU* 3.7 36.3 - - + -
151A PHE* 3.4 44.1 + + + -
154A ALA* 4.3 10.1 + - + -
155A PRO 3.0 28.7 + - - +
156A THR* 4.1 6.3 - - - +
157A GLY* 1.3 75.2 - - - +
159A LYS* 1.3 106.8 + - + +
161A SER* 3.2 4.9 + - - -
162A VAL* 3.1 37.4 + - + +
11D A 5.3 3.1 - - - +
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Residues in contact with LYS 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A LYS* 4.1 16.7 - - - +
141A TYR* 3.6 38.1 + - + +
145A LEU* 5.3 5.7 - - - +
156A THR* 3.6 9.8 + - - +
157A GLY 3.3 0.6 - - - -
158A TRP* 1.3 119.8 - - + +
160A ASN* 1.3 63.6 + - - +
162A VAL* 3.3 4.3 + - - +
163A ARG* 3.2 38.2 + - - +
2C T 4.8 9.9 + - - +
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Residues in contact with ASN 160 (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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156A THR* 3.4 17.7 + - - +
157A GLY* 3.1 13.8 + - - +
159A LYS* 1.3 78.8 - - - +
161A SER* 1.3 56.8 + - - +
163A ARG* 3.0 27.0 + - - +
164A HIS* 2.9 28.4 + - - +
164B HIS* 6.0 0.6 - - - -
3C A 5.3 0.2 - - - +
5C C 3.4 5.8 + - - +
12D C 3.5 15.1 + - + +
13D G 2.8 38.6 + - - +
14D C 4.0 7.1 - - - +
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Residues in contact with SER 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A PHE* 3.7 33.0 - - - -
157A GLY 3.2 11.7 + - - -
158A TRP 3.2 5.1 + - - -
160A ASN* 1.3 75.0 - - - +
162A VAL* 1.3 63.4 + - - +
164A HIS* 3.8 8.1 - - - +
165A ASN* 3.1 24.3 + - - +
10D G 4.0 5.6 - - - +
11D A 3.4 34.1 + - - -
12D C 3.7 5.8 + - - +
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Residues in contact with VAL 162 (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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119A PHE* 3.7 22.7 - - + -
123A ILE* 3.6 24.3 - - + +
137A VAL* 4.7 1.6 - - + -
140A ILE* 4.1 18.2 - - + -
141A TYR* 4.0 17.0 - - + -
144A ILE* 4.5 9.4 - - + -
158A TRP* 3.1 34.5 + - + +
159A LYS 3.5 7.6 - - - +
160A ASN 3.2 0.2 - - - -
161A SER* 1.3 77.9 - - - +
163A ARG* 1.3 62.9 + - - +
165A ASN* 3.3 1.8 + - - -
166A LEU* 3.2 29.3 + - + +
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Residues in contact with ARG 163 (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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137A VAL* 3.6 13.5 - - + -
141A TYR* 2.8 45.4 + - - +
159A LYS* 3.2 23.5 + - - +
160A ASN* 3.0 34.6 - - - +
162A VAL* 1.3 76.5 - - - +
164A HIS* 1.3 62.7 + - - +
166A LEU* 3.4 10.1 + - + +
167A SER* 3.3 27.2 + - - -
189A TRP* 5.8 0.2 - - - -
2C T 5.7 1.2 - - - +
3C A 3.5 37.5 + - - +
4C G 2.8 48.2 + - + +
5C C 3.6 11.4 - - - +
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Residues in contact with HIS 164 (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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160A ASN 2.9 17.6 + - - +
161A SER* 3.8 9.6 - - - +
162A VAL 3.2 0.2 - - - -
163A ARG* 1.3 77.4 - - - +
165A ASN* 1.3 65.2 + - + +
167A SER* 3.6 1.4 + - - -
168A LEU* 3.1 52.5 + - + +
5C C 3.6 12.3 - - - +
6C G 3.3 32.1 + + - +
7C T 3.7 26.8 + - + -
8C C 5.7 0.2 - - - -
10D G 3.8 24.8 + + - -
11D A 4.0 14.8 - - - -
12D C 5.2 0.2 - - - -
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Residues in contact with ASN 165 (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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119A PHE* 4.2 9.5 - - + +
120A SER* 3.0 39.8 + - - +
123A ILE* 4.1 8.5 - - + -
161A SER 3.1 17.9 + - - +
162A VAL 3.7 4.5 - - - +
163A ARG 3.3 0.6 - - - -
164A HIS* 1.3 78.2 - - + +
166A LEU* 1.3 65.5 + - - +
168A LEU* 4.7 4.6 - - - +
169A ASN* 3.0 36.8 + - - +
172A PHE* 3.2 11.8 - - - -
9D A 5.4 3.0 + - - -
10D G 4.4 7.1 + - - -
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Residues in contact with LEU 166 (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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123A ILE* 3.6 34.5 - - + -
127A ILE* 5.2 0.2 - - + -
137A VAL* 4.1 22.0 - - + -
140A ILE* 4.2 9.9 - - + -
162A VAL* 3.2 18.6 + - + +
163A ARG* 3.7 8.7 - - - +
164A HIS 3.3 0.4 - - - -
165A ASN* 1.3 79.9 - - - +
167A SER* 1.3 52.3 + - - +
169A ASN 3.6 0.7 - - - +
172A PHE* 3.7 21.0 - - + +
189A TRP* 3.6 56.8 - - + +
301A MG 2.3 32.1 - - - -
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Residues in contact with SER 167 (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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163A ARG 3.3 15.4 + - - -
164A HIS* 4.3 1.8 - - - -
166A LEU* 1.3 77.4 - - - +
168A LEU* 1.3 62.7 + - - +
189A TRP* 4.2 6.2 - - - -
301A MG 3.6 6.7 - - - -
4C G 3.6 13.0 - - - +
5C C 2.5 53.2 + - - -
6C G 5.8 0.7 - - - -
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Residues in contact with LEU 168 (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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164A HIS* 3.1 48.3 + - + +
165A ASN* 4.3 4.3 - - - +
167A SER* 1.3 78.7 - - - +
169A ASN* 1.3 73.0 + - - +
170A LYS* 3.4 6.1 + - - +
6C G 6.1 1.3 - - - +
7C T 6.3 0.7 - - + -
9D A 5.4 11.0 - - + +
10D G 5.9 0.7 - - - +
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Residues in contact with ASN 169 (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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120A SER* 3.0 17.2 + - - -
165A ASN* 3.0 39.9 + - - +
166A LEU 3.6 0.2 - - - +
168A LEU* 1.3 85.8 - - - +
170A LYS* 1.3 61.9 + - - +
171A CYS* 3.4 26.5 + - - -
172A PHE* 3.5 8.9 + - + -
199A LEU* 5.8 0.4 - - - +
301A MG 2.3 31.2 - - - -
9D A 4.8 7.8 + - - -
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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