Contacts of the strand formed by residues 134 - 148 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78F LYS* 2.7 32.7 + - - +
74H VAL* 4.2 7.9 - - + -
75H SER 3.9 3.1 - - - +
76H ILE* 4.8 0.2 - - - +
77H ARG* 4.3 0.4 - - - -
86H PHE* 3.6 37.7 - - + -
128H LEU* 3.5 33.7 - - + +
129H LEU* 4.1 14.7 - - + +
131H HIS* 3.2 10.9 + - + +
132H HIS 3.4 0.2 - - - -
133H GLY* 1.3 76.5 - - - +
135H GLN* 1.3 61.2 + - - +
136H ASP 3.6 26.5 - - - +
137H ALA* 4.8 0.2 - - + -
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Residues in contact with GLN 135 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78F LYS* 4.4 18.1 - - + +
75H SER* 2.8 29.0 + - - +
76H ILE 3.4 20.6 - - - +
77H ARG* 3.8 14.7 - - + +
78H LYS* 4.2 17.5 - - - +
129H LEU* 5.4 0.9 - - - +
133H GLY 3.6 3.0 + - - -
134H VAL* 1.3 74.0 - - - +
136H ASP* 1.3 66.2 + - + +
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Residues in contact with ASP 136 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83F ARG* 5.7 1.0 + - - -
107F ASP* 3.7 11.8 - - - +
1005F CA 2.5 29.2 - - - -
74H VAL* 3.5 2.1 - - - -
75H SER* 2.9 37.4 + - - +
129H LEU* 4.2 11.9 - - - +
134H VAL* 3.5 11.4 - - - +
135H GLN* 1.3 85.9 - - + +
137H ALA* 1.3 80.4 + - - +
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Residues in contact with ALA 137 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103F THR 4.5 1.6 - - - +
104F GLY 3.9 7.1 - - - +
105F GLU* 5.4 0.3 - - - -
107F ASP* 5.5 0.3 - - - +
72H ILE* 4.2 6.7 - - + -
73H ARG 3.2 10.8 - - - +
74H VAL* 4.2 4.7 - - + -
124H VAL* 5.8 2.0 - - + -
128H LEU* 3.6 31.4 - - + -
129H LEU* 3.9 15.7 - - + +
134H VAL* 4.8 0.7 - - + -
136H ASP* 1.3 91.2 + - - +
138H GLN* 1.3 63.2 + - - +
139H SER* 5.2 0.9 - - - +
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Residues in contact with GLN 138 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
905E GOL 5.6 1.0 + - - -
103F THR 3.6 5.8 - - - -
104F GLY* 3.5 19.9 - - - +
105F GLU* 3.2 35.9 + - - +
73H ARG* 2.8 63.5 + - + +
105H GLU* 5.9 0.6 + - - -
137H ALA* 1.3 77.5 - - - +
139H SER* 1.3 61.8 + - - +
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Residues in contact with SER 139 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139E SER 5.3 2.4 - - - +
905E GOL 4.7 5.7 + - - -
103F THR* 3.1 20.8 + - - +
104F GLY* 4.5 4.0 - - - -
103G THR* 5.0 0.2 + - - -
70H ALA* 5.0 0.2 - - - -
71H PHE 3.3 9.2 - - - -
72H ILE* 3.4 19.2 - - - +
120H PHE* 3.3 32.0 - - - -
124H VAL* 5.0 1.4 - - - +
137H ALA* 5.2 0.9 - - - +
138H GLN* 1.3 80.0 - - - +
140H SER* 1.3 65.8 + - - +
141H PHE* 4.0 17.2 - - - -
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Residues in contact with SER 140 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102G LEU* 4.2 23.9 - - - +
103G THR* 3.6 8.3 - - - -
104G GLY* 3.5 26.2 + - - -
70H ALA* 3.4 5.0 - - - +
71H PHE* 2.8 36.2 + - - -
73H ARG* 5.8 2.7 + - - -
139H SER* 1.3 74.4 + - - +
141H PHE* 1.3 66.6 + - - +
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Residues in contact with PHE 141 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117E MSE 4.3 7.2 - - + -
141E PHE* 3.7 27.8 - + - -
103F THR* 3.9 12.8 - - + -
102G LEU* 3.2 8.2 - - - -
103G THR* 2.8 50.3 + - + +
68H LEU* 3.7 28.9 - - + -
69H GLN 3.3 7.9 - - - +
70H ALA* 3.8 24.7 - - + -
71H PHE 4.9 0.2 - - - +
117H MSE 3.9 13.2 - - + -
120H PHE* 3.4 42.4 - + - -
139H SER* 4.0 14.8 - - - -
140H SER* 1.3 77.4 - - - +
142H VAL* 1.3 62.1 + - - +
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Residues in contact with VAL 142 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117E MSE 4.0 17.4 - - - +
121E SER* 5.3 0.5 - - - -
907E GOL 5.1 12.7 + - - +
100G PHE* 3.8 25.6 - - + -
101G ALA 3.5 4.3 - - - +
102G LEU* 3.7 15.9 - - + -
69H GLN* 3.0 44.3 + - + +
71H PHE* 3.8 7.0 - - + -
141H PHE* 1.3 70.5 - - - +
143H LEU* 1.3 62.8 + - - +
144H LYS* 3.7 27.6 - - - +
145H GLU* 4.0 4.7 - - + +
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Residues in contact with LEU 143 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117E MSE 3.3 24.5 - - + -
120E PHE* 3.9 9.2 - - + -
121E SER* 2.5 46.4 + - - +
124E VAL* 4.1 22.9 - - + -
125E LEU* 4.1 15.3 - - + +
129E LEU* 5.2 3.6 - - + -
907E GOL 4.1 10.1 + - - -
83G ARG* 5.8 1.3 - - - +
101G ALA* 2.6 19.6 + - + +
102G LEU 3.1 26.9 - - - +
103G THR* 3.6 16.2 - - + -
141H PHE 3.4 0.6 + - - -
142H VAL* 1.3 74.2 - - - +
144H LYS* 1.3 60.2 + - - +
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Residues in contact with LYS 144 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125E LEU* 4.0 21.1 - - + -
907E GOL 5.9 2.7 - - - -
91G ARG* 5.8 4.3 - - - +
100G PHE* 3.5 2.6 - - - -
101G ALA* 2.8 37.5 + - + +
142H VAL* 3.5 7.5 - - - +
143H LEU* 1.3 82.7 - - - +
145H GLU* 1.3 69.8 + - - +
146H ILE* 3.6 22.0 + - + +
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Residues in contact with GLU 145 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53G ARG* 6.1 0.5 - - - -
91G ARG* 5.2 1.0 + - - -
100G PHE* 3.6 30.8 - - + -
61H PRO* 5.7 5.7 - - - +
62H GLU* 5.5 2.9 - - - +
69H GLN* 4.7 5.0 - - - +
142H VAL* 4.0 5.4 - - + +
144H LYS* 1.3 84.0 - - - +
146H ILE* 1.3 63.3 + - - +
147H LYS* 3.9 12.0 - - - +
148H HIS* 3.5 32.4 + - - +
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Residues in contact with ILE 146 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87G ALA* 3.2 45.3 - - + +
90G VAL* 3.5 16.4 - - + -
91G ARG* 3.2 33.1 + - + +
99G CYS* 3.0 20.6 + - - +
101G ALA* 4.5 0.7 - - + +
108G TYR* 3.8 32.3 - - + +
144H LYS* 3.7 39.5 - - + +
145H GLU* 1.3 74.8 - - - +
147H LYS* 1.3 60.7 + - - +
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Residues in contact with LYS 147 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90G VAL* 2.7 26.0 + - + +
91G ARG* 3.6 26.5 + - + -
93G TRP 2.6 33.9 + - - -
94G PRO* 4.4 2.6 - - - +
96G VAL* 2.6 26.1 + - + +
97G LEU 3.7 10.1 - - - +
98G SER* 3.2 2.8 - - - -
99G CYS* 2.8 38.1 + - + +
100G PHE* 4.4 0.5 - - - -
145H GLU* 3.9 5.4 - - - +
146H ILE* 1.3 83.7 - - + +
148H HIS* 1.3 67.6 + - - +
149H THR* 4.4 13.5 - - + +
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Residues in contact with HIS 148 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53G ARG* 3.4 40.8 + - - -
97G LEU 3.3 2.7 - - - -
98G SER* 3.6 16.9 - - - -
100G PHE* 4.3 10.3 - + + -
69H GLN* 6.2 0.4 - - - -
111H GLN* 5.2 7.6 - - - -
145H GLU* 3.5 32.3 + - + +
147H LYS* 1.3 79.1 - - - +
149H THR* 1.3 70.0 + - - +
150H THR* 5.2 10.9 - - + +
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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