Contacts of the helix formed by residues 162 - 180 (chain I) in PDB entry 1MWA
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 162 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C SER* 5.1 5.8 - - - -
52C GLY 5.4 3.6 - - - -
158I ALA* 2.7 18.1 + - - +
161I GLU* 1.3 74.9 - - - +
163I THR* 1.3 67.0 + - - -
164I CYS 3.0 2.4 + - - -
165I VAL* 3.3 3.5 + - - +
166I GLU* 2.7 40.7 + - - +
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Residues in contact with THR 163 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C TYR* 6.0 1.4 - - - -
50C TYR 5.4 2.4 + - - -
51C SER* 5.3 6.6 + - - -
158I ALA 3.1 5.0 + - - -
159I TYR* 3.0 39.8 + - + +
162I GLY* 1.3 68.7 - - - -
164I CYS* 1.3 66.3 + - - +
166I GLU* 3.1 17.8 + - - +
167I TRP* 2.9 24.2 + - + -
1Q GLU* 3.2 39.4 + - + +
2Q GLN 5.0 0.2 - - - +
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Residues in contact with CYS 164 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5I LEU* 3.7 21.4 - - - +
7I TYR* 6.2 0.2 - - - -
100I GLY* 4.0 5.6 - - - -
101I CYS* 2.0 52.0 - - + -
159I TYR* 2.4 51.2 + - + +
160I LEU* 3.5 13.0 - - - +
162I GLY 3.0 0.4 + - - -
163I THR* 1.3 63.5 - - - +
165I VAL* 1.3 68.4 + - - +
167I TRP* 2.6 17.2 + - - +
168I LEU* 2.9 10.7 + - - +
1Q GLU 5.5 0.2 - - - -
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Residues in contact with VAL 165 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269H PRO* 6.1 2.5 - - + -
101I CYS* 3.4 13.2 - - + -
103I VAL* 3.5 34.3 - - + -
107I GLY* 4.6 11.0 - - - +
108I ARG 5.6 0.9 - - - +
109I LEU* 4.8 8.3 - - + -
160I LEU 3.3 19.3 - - - +
161I GLU* 3.8 14.4 - - - +
162I GLY 3.3 5.1 + - - +
164I CYS* 1.3 78.1 - - - +
166I GLU* 1.3 63.5 + - + +
167I TRP 3.3 0.2 + - - -
168I LEU* 3.5 3.8 + - - +
169I ARG* 3.3 32.4 + - + +
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Residues in contact with GLU 166 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C THR* 5.2 10.7 + - - +
51C SER* 3.8 21.2 + - - -
162I GLY* 2.7 39.6 + - - +
163I THR* 3.1 16.8 + - - +
164I CYS 2.8 0.8 + - - -
165I VAL* 1.3 74.9 - - + +
167I TRP* 1.3 67.0 + - + +
169I ARG* 3.5 36.1 + - - +
170I ARG* 3.8 4.7 + - - +
1Q GLU* 5.6 0.2 - - - +
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Residues in contact with TRP 167 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C SER 5.6 1.8 - - - -
28C ALA* 3.9 17.7 - - + +
29C THR 5.6 0.6 - - - +
5I LEU* 4.1 2.0 - - + -
55I GLU* 3.8 23.1 - - - -
59I TYR* 4.3 5.6 - + + -
62I ARG* 3.1 27.4 - - - -
163I THR* 2.9 23.2 + - + +
164I CYS 2.6 11.5 + - - +
166I GLU* 1.3 75.2 + - + +
168I LEU* 1.3 56.5 + - - +
169I ARG 2.9 2.7 - - - -
170I ARG* 2.6 50.5 + - + +
171I TYR* 3.2 35.3 + + + -
1Q GLU* 2.5 59.0 + - + +
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Residues in contact with LEU 168 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3I HIS* 4.0 1.8 - - + -
4I SER* 2.8 48.5 - - - +
5I LEU* 3.6 23.1 - - + +
28I VAL* 4.3 3.1 - - + -
101I CYS* 4.4 2.5 - - - +
103I VAL* 3.5 40.4 - - + -
164I CYS 2.9 8.5 + - - +
165I VAL* 3.7 9.9 - - - +
167I TRP* 1.3 76.2 - - - +
169I ARG* 1.3 62.4 + - - +
171I TYR* 3.6 5.0 + - - +
172I LEU* 3.3 45.7 + - + +
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Residues in contact with ARG 169 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267H PRO* 4.3 10.6 + - - +
268H GLU* 3.4 48.7 + - - +
269H PRO* 4.4 11.3 - - - +
165I VAL* 3.3 19.4 + - - +
166I GLU* 3.5 37.9 + - - +
167I TRP 2.9 0.2 - - - -
168I LEU* 1.3 81.2 - - - +
170I ARG* 1.3 57.7 + - - +
172I LEU* 3.6 11.4 - - - +
173I LYS* 3.0 24.5 + - + +
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Residues in contact with ARG 170 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54I GLN* 5.0 10.7 + - - +
55I GLU* 2.8 34.3 + - - +
166I GLU 3.8 3.4 + - - +
167I TRP* 2.6 42.0 + - + +
169I ARG* 1.3 71.8 - - - +
171I TYR* 1.3 70.3 + - + +
173I LYS* 2.7 52.1 + - - +
174I ASN* 3.1 31.0 + - - +
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Residues in contact with TYR 171 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5I LEU* 3.3 45.5 - - + -
7I TYR* 3.6 5.4 + - - -
28I VAL* 3.7 14.1 - - + -
33I PHE* 3.3 27.1 - + - -
51I TRP* 4.0 15.7 - - + -
52I MET* 3.6 15.9 - - + -
55I GLU* 4.7 1.1 - - - -
59I TYR* 3.5 23.9 + + - -
63I GLU* 5.9 0.2 - - - +
167I TRP* 3.2 32.8 + + - -
168I LEU* 3.9 4.5 - - - +
170I ARG* 1.3 79.7 - - + +
172I LEU* 1.3 56.5 - - + +
174I ASN* 3.1 1.7 + - - +
175I GLY* 2.8 33.6 + - - -
179I LEU* 5.3 0.7 - - - -
1Q GLU* 2.7 32.5 + - - -
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Residues in contact with LEU 172 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3I HIS* 4.0 28.3 - - + +
28I VAL* 3.4 32.1 - - + -
29I ASP* 4.7 5.2 - - - +
103I VAL* 5.8 1.8 - - + -
168I LEU* 3.3 39.8 + - + +
169I ARG* 3.6 9.0 - - - +
171I TYR* 1.3 77.9 - - - +
173I LYS* 1.3 63.4 + - - +
176I ASN* 2.9 31.9 + - - +
179I LEU* 3.8 11.4 - - + -
180I LEU* 6.0 4.7 - - + -
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Residues in contact with LYS 173 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169I ARG* 3.0 15.6 + - + +
170I ARG* 2.7 51.9 + - - +
172I LEU* 1.3 72.8 - - - +
174I ASN* 1.3 64.4 + - - +
176I ASN* 4.1 8.2 - - - +
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Residues in contact with ASN 174 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51I TRP* 4.0 26.4 - - + +
52I MET* 5.9 2.4 - - + +
54I GLN* 3.9 26.3 - - + +
55I GLU* 4.7 3.3 - - - +
170I ARG* 3.1 39.3 + - - +
171I TYR* 3.1 6.4 + - - +
173I LYS* 1.3 86.7 + - - +
175I GLY* 1.3 58.0 + - - +
176I ASN* 3.0 9.6 + - - +
177I ALA* 4.7 2.9 + - - +
178I THR* 5.3 0.5 + - - -
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Residues in contact with GLY 175 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51I TRP* 3.4 35.9 - - - -
171I TYR 2.8 17.1 + - - -
172I LEU 3.8 1.8 - - - -
174I ASN* 1.3 72.7 - - - +
176I ASN* 1.3 67.8 + - - +
177I ALA 3.6 0.7 - - - -
178I THR* 3.2 4.8 + - - -
179I LEU* 2.8 28.3 + - - +
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Residues in contact with ASN 176 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172I LEU* 2.9 20.9 + - - +
173I LYS* 4.1 9.8 + - - +
174I ASN 3.0 5.1 + - - +
175I GLY* 1.3 79.4 - - - +
177I ALA* 1.3 72.1 + - - +
179I LEU* 3.1 7.1 + - - -
180I LEU* 3.1 33.0 + - - +
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Residues in contact with ALA 177 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174I ASN 4.7 2.5 + - - +
175I GLY 3.6 0.2 - - - -
176I ASN* 1.3 83.3 + - - +
178I THR* 1.3 65.6 + - - +
180I LEU 3.0 20.1 - - - +
181I ARG* 4.0 4.9 - - - +
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Residues in contact with THR 178 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31I THR* 6.0 4.0 - - + -
49I ALA* 5.4 1.3 - - + -
51I TRP* 3.2 39.5 - - + +
174I ASN 5.3 0.5 + - - -
175I GLY* 3.2 9.2 + - - -
176I ASN 2.9 1.2 + - - -
177I ALA* 1.3 79.3 - - - +
179I LEU* 1.3 67.7 + - + +
181I ARG* 2.9 27.1 - - + +
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Residues in contact with LEU 179 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28I VAL* 3.3 39.3 - - + +
29I ASP* 4.7 10.8 - - + +
31I THR* 3.5 39.7 - - + +
51I TRP* 4.6 17.5 - - + +
172I LEU* 3.8 18.4 - - + -
175I GLY 2.8 26.5 + - - +
176I ASN* 4.0 1.8 - - - +
178I THR* 1.3 75.2 - - + +
180I LEU* 1.3 71.1 + - + +
181I ARG* 3.1 11.6 + - - +
209I TYR* 4.7 9.6 + - - -
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Residues in contact with LEU 180 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3I HIS* 4.3 29.4 - - + +
29I ASP* 5.5 2.0 - - - +
172I LEU* 6.0 4.3 - - + -
176I ASN* 3.1 36.0 + - - +
177I ALA* 3.0 13.8 - - - +
179I LEU* 1.3 91.2 - - + +
181I ARG* 1.3 57.5 + - - +
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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