Contacts of the strand formed by residues 134 - 148 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A LYS* 2.9 32.2 + - - -
74G VAL* 3.9 11.2 - - + -
75G SER 3.9 2.9 - - - -
76G ILE* 4.9 0.4 - - + +
77G ARG* 3.6 2.5 - - - -
86G PHE* 3.6 37.2 - - + -
128G LEU* 3.5 32.1 - - + +
129G LEU* 4.3 13.0 - - + +
131G HIS* 2.9 13.9 + - + +
132G HIS 3.3 0.4 - - - -
133G GLY* 1.3 76.1 - - - +
135G GLN* 1.3 62.1 + - - +
136G ASP* 3.8 25.4 - - - +
137G ALA* 4.9 0.2 - - + -
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Residues in contact with GLN 135 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LYS* 4.2 16.1 - - + +
135E GLN* 4.5 14.0 + - - -
75G SER* 2.9 31.7 + - - +
76G ILE 3.7 19.9 - - - +
77G ARG* 3.9 19.2 - - + +
78G LYS 5.1 0.2 + - - -
129G LEU* 5.6 1.0 - - - +
133G GLY 3.7 2.6 + - - -
134G VAL* 1.3 73.9 - - - +
136G ASP* 1.3 70.3 + - + +
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Residues in contact with ASP 136 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A SER* 4.7 4.5 + - - -
83A ARG* 5.8 1.2 + - - -
107A ASP* 3.7 14.3 - - - +
1004A CA 2.6 29.5 - - - -
74G VAL* 3.5 5.5 - - - +
75G SER* 2.8 41.3 + - - +
129G LEU* 4.5 9.4 - - - +
134G VAL* 3.6 6.4 - - - -
135G GLN* 1.3 89.6 - - + +
137G ALA* 1.3 72.9 + - - +
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Residues in contact with ALA 137 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A THR 4.7 0.9 - - - +
104A GLY 3.7 7.6 - - - +
105A GLU* 5.3 0.5 - - - -
107A ASP* 5.5 0.2 - - - +
72G ILE* 4.0 7.4 - - + -
73G ARG 3.2 10.3 - - - +
74G VAL* 4.3 3.8 - - + -
124G VAL* 5.7 3.4 - - + -
128G LEU* 3.7 30.5 - - + -
129G LEU* 3.9 16.8 - - + +
134G VAL* 4.9 0.7 - - + -
136G ASP* 1.3 90.5 + - - +
138G GLN* 1.3 63.0 + - - +
139G SER* 5.2 0.7 - - - +
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Residues in contact with GLN 138 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A THR 3.5 6.3 - - - -
104A GLY* 3.5 20.1 - - - +
105A GLU* 3.4 34.4 + - - +
73G ARG* 2.8 73.0 + - + +
137G ALA* 1.3 76.7 - - - +
139G SER* 1.3 59.9 + - - +
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Residues in contact with SER 139 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A THR* 3.0 22.2 + - - +
104A GLY* 4.4 3.7 - - - -
139B SER 5.3 4.5 - - - +
71G PHE 3.4 9.0 - - - -
72G ILE* 3.4 19.6 - - - +
120G PHE* 3.3 32.8 - - - -
124G VAL* 5.0 1.2 - - - +
137G ALA* 5.3 0.5 - - - +
138G GLN* 1.3 77.9 + - - +
140G SER* 1.3 65.6 + - - +
141G PHE* 4.0 17.2 - - - -
103H THR* 4.8 0.7 + - - -
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Residues in contact with SER 140 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70G ALA* 3.4 5.5 - - - +
71G PHE* 2.8 35.7 + - - +
73G ARG* 5.3 9.7 + - - -
139G SER* 1.3 75.6 + - - +
141G PHE* 1.3 66.5 + - - +
102H LEU* 4.2 24.4 - - - +
103H THR* 3.6 10.8 - - - -
104H GLY* 3.9 20.9 + - - -
105H GLU 5.2 0.2 + - - -
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Residues in contact with PHE 141 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A THR* 4.0 10.1 - - + -
117B MSE 3.9 12.3 - - + -
141B PHE* 3.7 28.7 - + - -
68G LEU* 3.3 37.5 - - + -
69G GLN 3.3 5.8 - - - +
70G ALA* 3.7 25.1 - - + -
117G MSE 3.8 8.1 - - + -
120G PHE* 3.5 32.3 - + - -
139G SER* 4.0 18.6 - - - -
140G SER* 1.3 78.4 - - - +
142G VAL* 1.3 63.6 + - - +
143G LEU 3.3 0.5 + - - -
102H LEU* 3.4 7.0 - - - -
103H THR* 3.0 49.1 + - + +
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Residues in contact with VAL 142 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B MSE 4.6 13.9 - - - +
121B SER* 5.3 1.0 - - - -
67G GLY 5.6 0.9 - - - +
68G LEU* 6.0 0.2 - - - +
69G GLN* 3.0 51.3 + - + +
71G PHE* 3.8 20.4 - - + -
141G PHE* 1.3 72.4 - - - +
143G LEU* 1.3 60.0 + - - +
144G LYS* 3.3 33.9 - - - +
145G GLU* 3.9 3.1 - - + +
906G GOL 5.0 10.8 + - - +
100H PHE* 3.6 16.4 - - + -
101H ALA 3.6 5.8 - - - +
102H LEU* 4.0 2.7 - - + -
103H THR* 5.0 0.2 - - - -
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Residues in contact with LEU 143 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B MSE 4.8 1.8 - - - -
120B PHE* 3.9 15.9 - - + -
121B SER* 2.6 49.4 + - - +
124B VAL* 4.1 14.6 - - + -
125B LEU* 4.1 26.6 - - + +
129B LEU* 5.3 2.0 - - + -
141G PHE 3.3 0.6 + - - -
142G VAL* 1.3 74.1 - - - +
144G LYS* 1.3 62.6 + - - +
906G GOL 4.1 11.4 + - - -
83H ARG* 5.8 0.7 - - - +
101H ALA* 2.8 14.3 + - + +
102H LEU 3.3 24.9 - - - +
103H THR* 3.5 29.2 - - + -
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Residues in contact with LYS 144 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B LEU* 4.0 21.1 - - + -
142G VAL* 3.3 7.4 - - - +
143G LEU* 1.3 84.1 - - - +
145G GLU* 1.3 70.2 + - - +
146G ILE* 3.7 20.7 + - + -
906G GOL 5.3 2.2 - - - -
84H GLU* 5.3 6.7 + - - -
91H ARG* 5.2 6.3 - - - +
100H PHE* 3.5 4.2 - - - -
101H ALA* 2.9 37.1 + - + +
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Residues in contact with GLU 145 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69G GLN* 4.9 3.3 - - - +
142G VAL* 3.9 3.8 - - + +
144G LYS* 1.3 81.4 - - - +
146G ILE* 1.3 63.7 + - - +
147G LYS* 3.8 18.1 - - - +
148G HIS* 3.4 33.7 + - - +
91H ARG* 4.9 2.3 + - - -
100H PHE* 3.9 24.7 - - + -
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Residues in contact with ILE 146 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144G LYS* 4.1 34.5 - - + +
145G GLU* 1.3 77.6 - - - +
147G LYS* 1.3 61.6 + - + +
87H ALA* 3.6 44.4 - - + +
90H VAL* 4.7 4.9 - - + -
91H ARG* 3.0 34.7 + - - +
99H CYS* 2.9 33.4 + - + +
101H ALA* 4.3 0.7 - - + +
108H TYR* 3.7 32.5 - - + +
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Residues in contact with LYS 147 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145G GLU* 3.6 6.9 - - - +
146G ILE* 1.3 82.2 - - - +
148G HIS* 1.3 68.0 + - - +
149G THR* 4.2 16.4 - - + -
90H VAL* 3.0 29.6 + - + +
91H ARG* 3.8 25.3 + - + +
93H TRP 2.6 25.7 + - - -
94H PRO* 4.4 3.4 - - - +
96H VAL* 2.6 31.0 + - + +
97H LEU 3.6 8.7 - - - +
98H SER* 3.3 2.1 - - - -
99H CYS* 2.9 37.0 + - + +
100H PHE* 4.4 1.2 - - - -
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Residues in contact with HIS 148 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69G GLN* 6.0 0.9 + - - -
111G GLN* 5.3 6.5 + - - -
145G GLU* 3.4 32.8 + - + +
147G LYS* 1.3 78.4 - - - +
149G THR* 1.3 65.0 + - - +
150G THR* 5.1 14.4 - - + +
53H ARG* 3.7 32.5 + - - -
97H LEU 3.4 2.9 - - - -
98H SER* 3.2 24.2 - - - -
100H PHE* 4.3 12.6 - + + -
150H THR* 6.2 2.4 - - + +
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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