Contacts of the helix formed by residues 153 - 172 (chain A) in PDB entry 5W6V
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 PRO 153 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A MET* 4.3 18.8 - - + +
141A LEU* 3.8 31.0 - - + +
144A ALA* 4.2 5.8 - - + -
150A ILE* 4.8 1.8 - - + -
151A PRO* 3.1 10.9 - - + +
152A VAL* 1.3 80.8 - - - +
154A LEU* 1.3 65.0 + - - +
155A GLU* 3.2 4.3 - - + +
156A SER* 3.0 35.7 + - - +
157A VAL* 3.1 13.7 + - - +
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Residues in contact with LEU 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A VAL* 3.0 20.7 + - + +
153A PRO* 1.3 72.7 - - - +
155A GLU* 1.3 57.9 + - - +
157A VAL* 3.2 10.5 + - + +
158A GLN* 2.8 34.3 + - - +
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Residues in contact with GLU 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A HIS* 3.5 31.5 + - - -
99A TYR* 4.1 5.0 + - - -
133A LEU* 6.4 0.4 - - - -
136A VAL* 3.5 25.6 - - + +
153A PRO* 3.2 3.3 - - + -
154A LEU* 1.3 77.6 - - - +
156A SER* 1.3 61.9 + - - +
158A GLN* 3.9 18.5 + - - +
159A ALA* 3.2 18.7 + - - +
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Residues in contact with SER 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A VAL* 3.5 12.1 - - - +
137A SER 2.7 30.5 + - - -
138A TRP* 3.2 17.1 + - - -
140A MET* 5.0 0.2 - - - +
141A LEU* 3.8 17.5 - - - +
153A PRO* 3.0 28.5 + - - +
155A GLU* 1.3 78.2 - - - +
157A VAL* 1.3 64.1 + - - +
159A ALA 3.6 0.5 + - - -
160A LEU* 3.2 19.4 + - - +
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Residues in contact with VAL 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A LEU* 3.9 14.8 - - + -
152A VAL* 3.7 24.5 - - + -
153A PRO 3.1 14.5 + - - +
154A LEU* 3.7 13.5 - - + +
156A SER* 1.3 73.6 - - - +
158A GLN* 1.3 65.3 + - - +
160A LEU* 3.3 5.5 + - - +
161A ASP* 3.1 23.0 + - + +
204A VAL* 3.7 19.0 - - + +
206A PRO* 4.8 7.2 - - + -
211A MET* 3.7 26.2 - - + -
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Residues in contact with GLN 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A HIS* 4.8 0.3 - - - -
93A ASP* 5.1 0.7 - - - +
97A ASN* 3.8 20.4 + - - +
99A TYR* 2.9 23.6 + - - +
154A LEU* 2.8 21.7 + - - +
155A GLU* 3.9 22.7 + - - +
157A VAL* 1.3 74.3 - - - +
159A ALA* 1.3 62.2 + - - +
161A ASP* 3.2 6.7 + - - +
162A VAL* 3.0 35.4 + - + +
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Residues in contact with ALA 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A VAL* 4.2 12.6 - - + -
91A VAL* 5.1 1.0 - - - +
99A TYR* 3.6 42.2 - - + +
136A VAL* 4.3 1.1 - - + -
138A TRP* 4.2 13.7 - - + +
155A GLU 3.2 16.3 + - - +
156A SER 4.0 3.8 - - - +
157A VAL 3.4 0.2 - - - -
158A GLN* 1.3 78.7 - - - +
160A LEU* 1.3 60.9 + - - +
162A VAL* 3.6 2.4 + - - +
163A ALA* 3.3 22.5 + - - +
395A PHE* 6.1 0.5 - - - -
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Residues in contact with LEU 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A VAL* 4.3 4.3 - - + -
47A ILE* 3.7 33.7 - - + -
138A TRP* 3.8 15.0 - - + +
141A LEU* 4.7 1.6 - - + -
156A SER 3.2 16.4 + - - +
157A VAL 3.7 5.6 - - - +
158A GLN 3.2 0.2 - - - -
159A ALA* 1.3 79.6 - - - +
161A ASP* 1.3 61.9 + - - +
163A ALA* 3.5 1.8 + - - +
164A MET* 3.2 42.1 + - - +
204A VAL* 3.9 23.3 - - + -
211A MET* 4.0 24.7 - - + -
397A ILE* 3.6 29.2 - - + -
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Residues in contact with ASP 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A VAL* 3.1 15.9 + - + +
158A GLN* 3.7 6.3 - - - +
160A LEU* 1.3 75.2 - - - +
162A VAL* 1.3 64.9 + - + +
164A MET* 3.4 1.1 + - - -
165A ARG* 2.9 55.2 + - - +
177A ARG* 6.0 1.4 + - - +
202A GLN* 4.6 2.9 + - - -
203A SER* 4.6 2.6 - - - -
204A VAL* 3.8 39.9 + - + +
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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
----------------------------------------------------------
91A VAL* 4.0 3.1 - - + -
92A TYR 3.6 38.3 - - - +
93A ASP* 3.9 21.1 - - + +
99A TYR* 4.0 27.1 - - + -
158A GLN* 3.0 26.4 + - + +
159A ALA 3.9 4.9 - - - +
160A LEU 3.4 0.2 - - - -
161A ASP* 1.3 77.6 - - + +
163A ALA* 1.3 56.1 + - - +
165A ARG* 3.7 8.7 - - - +
166A HIS* 3.0 29.1 + - - +
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Residues in contact with ALA 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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91A VAL* 3.7 29.8 - - + +
138A TRP* 5.2 0.9 - - + -
159A ALA 3.3 14.6 + - - +
160A LEU* 3.9 4.5 - - - +
162A VAL* 1.3 81.8 - - - +
164A MET* 1.3 61.8 + - - +
165A ARG 3.2 1.4 + - - -
166A HIS* 3.4 11.8 + - - +
167A LEU 4.8 0.5 + - - -
389A ASP* 5.0 1.2 - - - +
391A TYR* 4.3 11.3 - - - +
392A ILE* 4.3 5.8 - - - +
395A PHE* 4.2 14.8 - - + -
397A ILE* 4.2 19.3 - - + -
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Residues in contact with MET 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A VAL* 3.9 27.1 - - + -
160A LEU* 3.2 28.7 + - + +
161A ASP* 3.4 4.5 + - - +
162A VAL 3.4 0.4 - - - -
163A ALA* 1.3 75.2 - - - +
165A ARG* 1.3 56.6 + - - +
166A HIS 3.7 0.2 - - - -
167A LEU* 5.4 0.3 + - - +
168A ALA* 5.6 1.4 + - - +
202A GLN* 2.9 20.5 + - - +
204A VAL* 3.9 22.0 - - + -
213A LEU* 3.8 25.1 - - + -
386A TYR* 3.8 16.8 - - + -
389A ASP* 4.7 4.2 - - - +
392A ILE* 4.0 19.9 - - + +
397A ILE* 4.3 10.8 - - + -
399A VAL* 3.7 29.8 - - + -
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Residues in contact with ARG 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ARG* 6.2 0.2 - - - +
92A TYR 6.0 0.7 - - - +
161A ASP* 2.9 50.1 + - - +
162A VAL* 3.8 9.4 - - - +
163A ALA 3.1 0.2 - - - -
164A MET* 1.3 76.1 - - - +
166A HIS* 1.3 66.8 + - - +
167A LEU 3.3 2.9 - - - -
168A ALA* 3.4 7.3 + - - +
169A SER* 3.0 31.3 + - - +
176A GLY 4.4 2.6 + - - -
177A ARG* 3.1 45.4 + - - +
179A PHE* 3.5 27.1 - - + -
202A GLN* 2.9 38.8 + - - +
203A SER* 4.5 0.2 - - - +
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Residues in contact with HIS 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ARG* 5.4 1.7 + - + -
73A VAL* 6.0 2.2 - - + -
74A GLU* 4.7 6.5 + - - -
90A PRO 3.9 2.4 + - - -
91A VAL* 3.7 21.3 - - + -
92A TYR* 2.9 44.7 + + + +
162A VAL 3.0 16.7 + - - +
163A ALA 3.4 5.4 + - - +
165A ARG* 1.3 78.4 - - - +
167A LEU* 1.3 62.4 + - - +
169A SER* 3.3 12.8 + - - -
170A MET* 3.3 37.7 + - + +
391A TYR* 3.4 48.4 + + + -
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Residues in contact with LEU 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 ALA 4.8 0.6 + - - -
164A MET 5.4 0.4 + - - +
165A ARG 3.3 0.8 - - - -
166A HIS* 1.3 79.0 - - - +
168A ALA* 1.3 65.8 + - - +
170A MET* 3.0 20.3 + - + +
171A ARG* 3.2 39.4 + - + +
389A ASP* 3.5 39.3 + - + +
390A PRO* 4.5 11.7 - - + -
391A TYR* 3.9 24.8 - - + -
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Residues in contact with ALA 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 MET 5.6 0.9 + - - +
165A ARG* 3.4 8.6 + - - +
166A HIS 3.4 0.4 - - - -
167A LEU* 1.3 79.5 - - - +
169A SER* 1.3 58.0 + - - +
171A ARG* 4.5 0.9 - - - +
172A TYR* 2.9 60.5 + - + +
179A PHE* 3.7 28.3 - - + -
200A PHE* 4.5 5.6 - - + -
202A GLN* 5.1 3.6 - - - +
386A TYR* 6.2 2.0 - - + -
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Residues in contact with SER 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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67A ARG* 6.1 0.2 - - - -
70A ARG* 3.4 52.2 + - - -
165A ARG* 3.0 26.2 + - - +
166A HIS* 3.5 7.2 - - - -
167A LEU 3.2 0.4 - - - -
168A ALA* 1.3 76.0 - - - +
170A MET* 1.3 59.4 + - - +
171A ARG 3.5 0.2 - - - -
172A TYR 4.0 9.1 - - - +
174A PRO* 4.3 10.1 - - - +
179A PHE* 3.5 18.1 - - - -
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Residues in contact with MET 170 (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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70A ARG* 3.6 38.6 - - + +
71A GLU* 5.0 3.4 - - + +
74A GLU* 3.8 39.7 - - + +
92A TYR* 6.3 0.2 - - - -
166A HIS* 3.3 37.9 - - + +
167A LEU* 3.0 13.6 + - + +
169A SER* 1.3 76.4 - - - +
171A ARG* 1.3 78.3 + - - +
172A TYR 3.8 1.6 - - - -
391A TYR* 5.9 0.4 - - - +
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Residues in contact with ARG 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A LEU* 3.7 36.4 - - + +
168A ALA* 3.2 2.9 + - - +
170A MET* 1.3 97.2 + - + +
172A TYR* 1.3 80.9 + - + +
181A SER* 5.8 0.3 - - - -
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Residues in contact with TYR 172 (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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168A ALA* 2.9 39.7 + - + +
169A SER 4.0 7.6 - - - +
170A MET 4.9 0.9 - - - -
171A ARG* 1.3 95.2 + - + +
173A THR* 1.3 64.8 + - - +
174A PRO* 3.2 12.0 - - - +
179A PHE* 3.6 24.2 - - + -
180A PHE 3.6 8.3 - - - +
181A SER* 4.2 24.7 - - - +
200A PHE* 4.0 20.8 - + - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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