Contacts of the helix formed by residues 148 - 162 (chain P) in PDB entry 3V3K
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 SER 148 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175O GLY* 3.2 30.5 - - - -
177O ARG* 5.0 1.3 - - - +
144P PRO* 3.6 11.5 - - - +
145P HIS* 2.7 28.7 + - - -
146P HIS 3.3 0.4 - - - -
147P SER* 1.3 85.5 + - - +
149P GLU* 1.3 64.1 + - - +
150P LEU* 3.7 3.8 + - - -
151P TYR* 3.2 17.8 + - - +
152P GLY 3.8 2.6 + - - -
181P TYR* 3.6 19.6 - - - -
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Residues in contact with GLU 149 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175O GLY 4.5 1.8 - - - -
177O ARG* 6.5 0.2 - - - -
77P MET* 5.1 10.2 - - + +
80P ARG* 3.2 49.1 + - - +
81P ASN* 3.9 21.0 + - - +
148P SER* 1.3 73.1 - - - +
150P LEU* 1.3 66.5 + - - +
152P GLY* 3.3 11.6 + - - -
153P ASP* 3.4 5.5 + - - +
178P ASP 4.9 0.7 - - - +
181P TYR* 5.0 2.6 - - - -
183P LYS* 3.2 33.1 + - - +
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Residues in contact with LEU 150 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73P VAL* 4.1 26.5 - - + -
76P LEU* 4.2 17.0 - - + -
77P MET* 6.5 0.2 - - + -
80P ARG* 5.0 0.7 - - - +
110P TYR* 5.1 2.5 - - - +
114P LEU* 4.3 8.7 - - + -
117P LEU* 4.2 20.9 - - + -
141P LEU 4.4 9.9 - - - +
142P LEU* 5.9 0.2 - - - -
144P PRO* 4.0 22.0 - - + -
148P SER* 3.7 4.6 + - - +
149P GLU* 1.3 79.5 - - - +
151P TYR* 1.3 57.7 + - - +
153P ASP* 3.2 6.2 + - - +
154P LEU* 2.9 53.8 + - + +
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Residues in contact with TYR 151 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288O GLU* 3.5 46.3 + - - +
290O LYS* 4.4 4.1 + - - -
121P LYS* 6.4 0.4 - - - -
144P PRO* 3.7 29.5 - - + +
145P HIS 3.3 17.0 - - - +
146P HIS* 3.3 32.5 - - + -
148P SER* 3.2 9.1 + - - +
149P GLU 3.3 0.2 - - - -
150P LEU* 1.3 77.5 - - - +
152P GLY* 1.3 57.6 + - - +
154P LEU* 4.0 3.9 - - + +
155P ARG* 3.0 60.9 + - + +
181P TYR* 3.3 19.3 - + - -
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Residues in contact with GLY 152 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148P SER 3.8 4.0 + - - -
149P GLU 3.3 6.6 + - - -
151P TYR* 1.3 80.5 - - - +
153P ASP* 1.3 59.2 + - - +
155P ARG* 4.2 5.8 + - - +
156P ALA* 3.2 27.0 + - - +
178P ASP* 3.9 9.9 - - - +
181P TYR* 3.5 34.9 - - - -
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Residues in contact with ASP 153 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80P ARG* 2.8 29.1 + - - -
110P TYR* 2.7 34.7 + - - +
114P LEU* 3.7 22.6 - - + +
149P GLU 3.4 2.1 + - - +
150P LEU* 3.2 9.2 + - - +
152P GLY* 1.3 75.5 - - - +
154P LEU* 1.3 54.9 + - - +
156P ALA* 3.3 6.3 + - - +
157P MET* 2.7 36.6 + - - +
176P VAL 4.1 1.0 - - - +
177P PRO* 3.7 7.9 - - - +
178P ASP 3.1 27.2 + - - +
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Residues in contact with LEU 154 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114P LEU* 4.1 16.6 - - + +
117P LEU* 4.1 26.5 - - + -
118P HIS* 4.1 24.1 - - + +
121P LYS* 5.3 11.7 - - + +
142P LEU* 3.9 23.6 - - + +
144P PRO* 4.2 9.0 - - + -
150P LEU* 2.9 44.0 + - + +
151P TYR* 4.1 4.3 - - + +
153P ASP* 1.3 73.6 - - - +
155P ARG* 1.3 60.9 + - - +
157P MET* 3.4 4.4 + - + +
158P LYS* 3.0 28.1 + - - +
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Residues in contact with ARG 155 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290O LYS* 3.9 18.3 - - - +
383O TYR* 5.9 0.6 + - - -
151P TYR* 3.0 46.8 + - + +
152P GLY* 4.3 5.3 + - - +
154P LEU* 1.3 75.0 - - - +
156P ALA* 1.3 61.8 + - - +
158P LYS* 3.7 10.2 + - + +
159P CYS* 3.3 33.0 + - - -
167P ASP* 4.9 10.8 + - - +
168P PHE* 4.0 28.7 - - - -
178P ASP* 5.3 4.0 + - - -
181P TYR* 3.7 27.9 - - - -
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Residues in contact with ALA 156 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152P GLY 3.2 20.8 + - - +
153P ASP* 3.4 7.4 - - - +
154P LEU 3.3 0.2 - - - -
155P ARG* 1.3 75.6 - - - +
157P MET* 1.3 63.6 + - - +
159P CYS* 3.2 14.1 + - - +
160P LEU* 3.3 18.7 + - - +
174P ILE* 4.0 13.7 - - + +
175P ARG 3.2 28.0 - - - +
176P VAL* 4.5 3.6 - - - +
178P ASP* 4.6 5.2 - - + +
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Residues in contact with MET 157 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32P LEU* 4.4 11.2 - - - -
111P ILE* 4.9 3.4 - - - -
114P LEU* 3.4 35.0 - - + +
115P PHE* 3.3 50.3 - - + -
118P HIS* 3.7 20.4 - - + -
153P ASP 2.7 15.8 + - - +
154P LEU* 3.6 9.6 - - + +
156P ALA* 1.3 73.3 - - - +
158P LYS* 1.3 61.0 + - - +
160P LEU* 3.5 1.9 + - - +
161P VAL* 3.1 48.1 + - + +
176P VAL* 3.9 23.7 + - + -
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Residues in contact with LYS 158 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118P HIS* 3.6 19.9 - - + +
125P GLU* 5.5 6.4 + - - -
154P LEU 3.0 17.8 + - - +
155P ARG* 3.8 11.4 - - + +
156P ALA 3.3 0.2 - - - -
157P MET* 1.3 75.0 - - - +
159P CYS* 1.3 59.3 + - - +
162P GLU* 2.8 68.7 + - + +
165P SER* 6.0 2.7 - - - -
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Residues in contact with CYS 159 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155P ARG* 3.3 26.4 + - - -
156P ALA* 3.2 11.0 + - - +
158P LYS* 1.3 82.1 - - - +
160P LEU* 1.3 59.3 + - - +
163P GLY* 3.1 7.0 + - - -
164P CYS* 2.7 49.9 + - - +
165P SER* 5.0 2.7 - - - -
167P ASP* 4.7 10.3 - - - -
168P PHE* 6.6 0.2 - - - -
174P ILE* 3.7 28.4 - - + +
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Residues in contact with LEU 160 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29P VAL 4.3 1.1 - - - +
30P SER 3.2 32.3 - - - +
31P GLU* 5.8 0.4 - - - -
32P LEU* 4.3 22.2 - - + +
156P ALA 3.3 11.2 + - - +
157P MET* 4.1 4.9 - - - +
158P LYS 3.4 0.2 - - - -
159P CYS* 1.3 76.9 - - - +
161P VAL* 1.3 66.3 + - - +
163P GLY* 4.1 3.8 + - - -
174P ILE* 3.8 30.7 - - + +
176P VAL* 3.4 42.0 - - + +
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Residues in contact with VAL 161 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32P LEU* 4.1 10.1 - - + -
115P PHE* 4.1 18.2 - - + -
118P HIS* 3.7 24.0 - - + -
157P MET* 3.1 41.7 + - + +
158P LYS 4.2 0.2 - - - +
160P LEU* 1.3 79.8 - - - +
162P GLU* 1.3 67.7 + - + +
163P GLY* 3.3 1.5 + - - -
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Residues in contact with GLU 162 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118P HIS* 4.5 4.6 + - - +
122P VAL* 4.4 21.3 - - - +
158P LYS* 2.8 52.1 + - + +
161P VAL* 1.3 82.0 - - + +
163P GLY* 1.3 65.1 + - - +
165P SER* 5.1 0.8 + - - -
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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