Contacts of the strand formed by residues 134 - 148 (chain C) in PDB entry 2P5V
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 VAL 134 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74C VAL* 4.0 11.4 - - + -
75C SER 3.9 2.9 - - - -
76C ILE* 4.7 0.9 - - + +
77C ARG* 3.5 19.7 + - - -
86C PHE* 3.7 36.3 - - + -
128C LEU* 3.5 34.8 - - + +
129C LEU* 4.2 19.7 - - + +
131C HIS* 3.0 15.6 + - + +
133C GLY* 1.3 78.0 - - - +
135C GLN* 1.3 62.1 + - - +
136C ASP 3.7 24.9 - - - +
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Residues in contact with GLN 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C SER* 2.9 39.8 + - - +
76C ILE 3.6 16.8 - - - +
77C ARG* 3.8 15.9 - - + +
78C LYS* 4.6 8.7 + - - +
129C LEU* 5.4 0.7 - - - +
133C GLY 3.8 2.6 + - - -
134C VAL* 1.3 74.6 - - - +
136C ASP* 1.3 70.2 + - + +
78E LYS* 2.8 42.8 - - + +
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Residues in contact with ASP 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C VAL* 3.7 1.0 - - - -
75C SER* 2.8 31.4 + - - +
129C LEU* 4.2 9.2 - - - +
134C VAL* 3.6 9.5 - - - +
135C GLN* 1.3 96.9 + - + +
137C ALA* 1.3 79.7 + - - +
1002C CA 2.4 30.5 - - - -
78E LYS* 3.5 23.6 + - - +
83E ARG* 5.2 2.6 + - - -
107E ASP* 3.6 7.1 - - - +
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Residues in contact with ALA 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C ILE* 3.9 8.3 - - + -
73C ARG 3.3 11.7 - - - +
74C VAL* 4.2 4.5 - - + -
124C VAL* 5.9 2.0 - - + -
128C LEU* 3.8 29.4 - - + -
129C LEU* 3.8 17.6 - - + +
134C VAL* 4.8 0.4 - - + -
136C ASP* 1.3 91.3 + - - +
138C GLN* 1.3 62.1 + - - +
139C SER* 5.4 0.7 - - - +
103E THR 4.7 1.0 - - - +
104E GLY 3.9 7.3 - - - +
105E GLU* 5.5 0.2 - - - -
107E ASP* 5.3 0.7 - - - +
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Residues in contact with GLN 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C ILE 3.7 0.2 - - - -
73C ARG* 2.7 79.9 + - + +
137C ALA* 1.3 74.9 - - - +
139C SER* 1.3 61.8 + - - +
103E THR 3.5 5.4 - - - -
104E GLY 3.4 21.3 - - - +
105E GLU* 3.4 32.4 + - - +
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Residues in contact with SER 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C PHE 3.3 9.9 - - - -
72C ILE* 3.5 20.0 - - - +
73C ARG* 3.8 6.9 + - - +
120C PHE* 3.3 32.3 - - - -
124C VAL* 5.1 1.0 - - - +
137C ALA* 5.3 0.3 - - - +
138C GLN* 1.3 77.7 + - - +
140C SER* 1.3 65.3 + - - +
141C PHE* 4.0 15.9 - - - -
103D THR* 5.0 0.3 + - - -
103E THR* 2.9 22.4 + - - +
104E GLY* 4.6 2.9 - - - -
139F SER 5.4 3.6 - - - +
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Residues in contact with SER 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C ALA* 3.4 4.5 - - - +
71C PHE* 2.8 33.6 + - - +
73C ARG* 3.5 18.0 + - - +
139C SER* 1.3 75.7 + - - +
141C PHE* 1.3 63.3 + - - +
102D LEU* 4.2 16.6 - - - +
103D THR* 3.6 10.8 - - - -
104D GLY* 4.1 18.9 + - - +
903D GOL 3.8 20.3 + - - -
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Residues in contact with PHE 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C LEU* 3.5 23.8 - - + -
69C GLN 3.3 6.5 - - - +
70C ALA* 3.7 17.3 - - + -
117C MSE 3.9 13.5 - - + -
120C PHE* 3.5 53.4 - + - -
139C SER* 4.0 10.1 - - - -
140C SER* 1.3 76.9 - - - +
142C VAL* 1.3 61.0 + - - +
102D LEU* 3.4 9.0 - - - -
103D THR* 2.9 45.5 + - + +
103E THR* 3.9 15.7 - - + -
117F MSE 3.9 16.6 - - + -
141F PHE* 3.8 28.0 - + - -
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Residues in contact with VAL 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C GLN* 3.0 52.7 + - + +
71C PHE* 4.1 5.2 - - + -
141C PHE* 1.3 71.8 - - - +
143C LEU* 1.3 64.4 + - - +
144C LYS* 3.4 29.6 - - - +
145C GLU* 3.9 3.6 - - + +
100D PHE* 3.9 19.3 - - + -
101D ALA 3.6 5.2 - - - +
102D LEU* 4.0 11.0 - - + -
117F MSE 3.9 18.2 - - - +
121F SER* 5.3 0.5 - - - -
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Residues in contact with LEU 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C PHE 3.4 0.4 + - - -
142C VAL* 1.3 75.5 - - - +
144C LYS* 1.3 63.6 + - - +
83D ARG* 6.0 0.9 - - - +
101D ALA* 2.8 13.5 + - + +
102D LEU* 3.3 23.8 - - - +
103D THR* 3.4 29.8 - - + -
117F MSE 4.5 3.8 - - - -
120F PHE* 3.8 15.7 - - + -
121F SER* 2.5 50.5 + - - +
124F VAL* 4.0 22.7 - - + -
125F LEU* 4.0 18.8 - - + +
129F LEU* 5.6 1.1 - - + -
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Residues in contact with LYS 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C VAL* 3.4 6.9 - - - +
143C LEU* 1.3 82.6 - - - +
145C GLU* 1.3 70.3 + - - +
146C ILE* 3.6 15.6 + - + +
84D GLU* 4.4 15.2 + - - -
91D ARG* 6.2 0.9 - - - +
100D PHE* 3.5 3.6 - - - -
101D ALA* 2.9 40.8 + - + +
1014D CL 4.0 15.0 - - + -
125F LEU* 4.2 13.0 - - + -
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Residues in contact with GLU 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C PRO* 6.1 1.0 - - - +
69C GLN* 5.0 3.6 - - - +
142C VAL* 3.9 5.0 - - + +
144C LYS* 1.3 81.6 - - - +
146C ILE* 1.3 64.0 + - - +
147C LYS* 3.8 18.1 - - - +
148C HIS* 3.5 32.4 + - - +
91D ARG* 5.2 0.7 + - - -
100D PHE* 3.9 23.6 - - + -
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Residues in contact with ILE 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C LYS* 4.1 33.0 - - + +
145C GLU* 1.3 79.2 - - - +
147C LYS* 1.3 61.3 + - + +
87D ALA* 3.6 43.3 - - + +
90D VAL* 4.5 5.6 - - + -
91D ARG* 3.1 37.0 + - - +
99D CYS* 2.9 29.3 + - + +
108D TYR* 3.7 25.4 - - + -
1014D CL 4.1 12.8 - - + -
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Residues in contact with LYS 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C GLU* 3.5 8.0 - - - +
146C ILE* 1.3 81.3 - - - +
148C HIS* 1.3 69.7 + - - +
149C THR* 4.5 11.2 - - + +
90D VAL* 2.8 33.5 + - + +
91D ARG* 3.5 26.1 + - + +
93D TRP 2.7 31.7 + - - -
94D PRO* 4.4 2.4 - - - +
96D VAL* 2.8 20.8 + - + +
97D LEU 3.8 10.3 - - - +
98D SER* 3.1 2.1 - - - -
99D CYS* 2.8 41.1 + - + +
100D PHE* 4.3 1.0 - - - -
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Residues in contact with HIS 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C LEU* 6.4 0.4 - - + -
69C GLN* 6.3 0.7 - - - -
111C GLN* 5.4 7.6 + - - -
113C PHE* 6.5 1.6 - + - -
145C GLU* 3.5 30.4 + - + +
147C LYS* 1.3 80.8 - - - +
149C THR* 1.3 69.9 + - - +
150C THR* 5.0 12.5 - - + +
53D ARG* 3.6 35.7 + - - -
97D LEU 3.4 3.1 - - - -
98D SER* 3.7 18.4 - - - +
100D PHE* 4.3 11.0 - + + -
150D THR* 6.4 0.9 - - + -
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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