Contacts of the helix formed by residues 130 - 149 (chain A) in PDB entry 2YVE
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 ASP 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A ASP* 3.0 19.9 + - + +
127A LEU 3.5 0.4 + - - +
129A ASN* 1.3 79.5 - - - +
131A ALA* 1.3 61.8 + - - +
132A HIS* 3.1 13.6 + - - +
133A LYS* 3.1 40.9 + - + +
134A ARG* 3.0 28.6 + - - +
3001A CL 3.9 2.2 - - - -
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Residues in contact with ALA 131 (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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130A ASP* 1.3 71.8 - - - +
132A HIS* 1.3 62.2 + - - +
134A ARG* 3.3 26.1 + - - +
135A ALA* 3.0 20.8 + - - +
2003A GOL 3.0 18.5 + - - +
3001A CL 3.3 21.7 - - + +
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Residues in contact with HIS 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LEU* 5.0 13.3 - - + +
130A ASP* 3.1 9.6 + - - +
131A ALA* 1.3 78.8 - - - +
133A LYS* 1.3 68.4 + - - +
135A ALA* 3.1 6.9 + - - +
136A VAL* 3.0 43.9 + - + +
174A PRO* 4.0 25.6 - - + +
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Residues in contact with LYS 133 (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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122A PRO* 5.1 8.1 - - + -
123A ASP* 3.4 37.0 + - - +
124A THR* 4.7 1.3 - - - -
125A ASP* 3.1 27.7 + - - +
126A ASP* 5.4 0.2 - - - +
127A LEU* 4.2 16.8 - - + -
130A ASP* 3.1 35.4 + - + +
132A HIS* 1.3 80.4 + - - +
134A ARG* 1.3 58.2 + - - +
136A VAL* 3.3 7.5 + - + +
137A TYR* 2.8 29.5 + - + +
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Residues in contact with ARG 134 (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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127A LEU* 3.0 55.1 + - + +
128A GLU 3.3 17.8 + - - -
129A ASN 3.9 1.2 - - - -
130A ASP 3.0 21.6 + - - +
131A ALA* 3.6 30.9 - - - +
132A HIS 3.2 0.2 - - - -
133A LYS* 1.3 73.5 - - - +
135A ALA* 1.3 61.9 + - - +
137A TYR* 4.4 0.2 - - - -
138A LEU* 2.9 29.8 + - - +
2003A GOL 2.8 34.0 + - - +
164B ALA* 4.2 12.1 - - - -
165B MET* 3.7 12.2 - - - +
168B THR* 3.5 19.7 + - - +
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Residues in contact with ALA 135 (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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131A ALA 3.0 13.4 + - - +
132A HIS* 3.1 11.0 + - - +
134A ARG* 1.3 78.3 - - - +
136A VAL* 1.3 60.5 + - - +
138A LEU* 3.4 11.8 + - - +
139A VAL* 3.4 24.1 + - - +
172A LEU* 5.0 2.9 - - - +
174A PRO* 3.8 23.6 - - + +
2003A GOL 3.9 9.6 + - - +
168B THR* 5.5 0.2 - - - -
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Residues in contact with VAL 136 (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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78A LEU* 5.0 5.4 - - + -
81A LEU* 4.0 28.7 - - + +
122A PRO* 3.9 29.8 - - + -
132A HIS* 3.0 43.7 + - + +
133A LYS* 3.7 9.6 - - + +
135A ALA* 1.3 75.3 - - - +
137A TYR* 1.3 63.4 + - - +
139A VAL* 3.1 9.2 + - - +
140A GLN* 3.1 18.7 + - - +
174A PRO* 4.6 9.4 - - + -
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Residues in contact with TYR 137 (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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122A PRO* 3.6 35.0 + - + -
123A ASP 4.1 6.5 - - - -
124A THR* 3.2 30.6 - - + +
127A LEU* 4.1 15.9 - - + -
133A LYS* 2.8 18.7 + - + +
134A ARG* 4.0 0.4 - - - +
136A VAL* 1.3 75.0 - - - +
138A LEU* 1.3 59.5 + - - +
140A GLN* 3.2 15.9 + - + +
141A LEU* 2.8 51.3 + - + +
149B HIS* 2.6 41.9 + + - -
153B HIS* 3.9 11.8 + + - +
157B LEU* 4.6 6.7 - - + -
165B MET* 3.9 16.8 - - + -
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Residues in contact with LEU 138 (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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134A ARG 2.9 17.3 + - - +
135A ALA* 3.5 9.6 - - - +
136A VAL 3.2 0.2 - - - -
137A TYR* 1.3 78.1 - - - +
139A VAL* 1.3 62.8 + - - +
141A LEU* 3.3 3.1 + - + +
142A ALA* 3.0 23.7 + - - +
172A LEU* 4.0 22.7 - - + -
2003A GOL 6.4 0.2 - - - -
142B ALA* 3.9 7.6 - - + -
165B MET* 3.6 6.5 - - + +
168B THR* 4.0 25.1 - - + +
169B ILE* 3.8 29.4 - - + -
172B LEU* 3.8 35.7 - - + -
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Residues in contact with VAL 139 (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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81A LEU* 4.1 11.9 - - + -
85A VAL* 3.6 27.4 - - + -
135A ALA 3.6 12.6 - - - +
136A VAL* 3.1 9.1 + - - +
138A LEU* 1.3 77.0 - - - +
140A GLN* 1.3 62.1 + - - +
142A ALA* 3.3 3.7 + - - +
143A ALA* 3.0 22.2 + - - +
169A ILE* 3.8 11.5 - - + +
172A LEU* 3.9 36.1 - - + +
173A ILE* 3.8 30.3 - - + -
174A PRO* 4.9 0.2 - - + -
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Residues in contact with GLN 140 (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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81A LEU* 4.2 9.0 - - + +
84A VAL* 3.9 12.4 - - - +
85A VAL* 5.8 0.7 - - - -
88A LEU* 3.5 19.8 - - - +
121A ILE* 3.8 17.7 - - - +
122A PRO* 3.2 31.9 - - + +
136A VAL 3.1 12.9 + - - +
137A TYR* 3.2 21.5 + - + +
139A VAL* 1.3 78.8 - - - +
141A LEU* 1.3 56.0 + - - +
143A ALA* 3.3 4.0 + - - +
144A ASP* 2.9 64.2 + - - +
1001A MBT 5.9 0.6 - - - -
153B HIS* 3.9 16.0 - - + +
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Residues in contact with LEU 141 (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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137A TYR* 2.8 28.1 + - + +
138A LEU* 3.7 4.5 - - - +
140A GLN* 1.3 73.6 - - - +
142A ALA* 1.3 58.1 + - - +
144A ASP* 3.2 8.2 + - - +
145A GLY 2.9 23.2 + - - -
141B LEU 3.5 1.0 - - - +
142B ALA* 3.7 22.4 - - + +
145B GLY* 3.4 32.4 - - - +
146B LEU* 3.9 10.3 - - + +
149B HIS* 4.0 23.3 - - + -
165B MET* 3.7 42.2 - - + -
169B ILE* 4.3 10.8 - - + -
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Residues in contact with ALA 142 (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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138A LEU 3.0 16.5 + - - +
139A VAL* 3.7 5.2 - - - +
141A LEU* 1.3 77.4 - - - +
143A ALA* 1.3 61.6 + - - +
145A GLY* 3.1 2.9 + - - -
146A LEU 3.1 17.3 + - - -
169A ILE* 3.8 17.3 - - + +
172A LEU* 5.1 1.6 - - + -
138B LEU* 3.9 28.0 - - + -
141B LEU* 3.7 8.7 - - + +
142B ALA* 3.8 22.4 - - + +
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Residues in contact with ALA 143 (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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85A VAL* 4.0 30.7 - - + +
88A LEU* 3.8 25.8 - - + +
139A VAL 3.0 16.8 + - - +
140A GLN* 3.6 6.3 - - - +
142A ALA* 1.3 75.8 - - - +
144A ASP* 1.3 63.8 + - - +
146A LEU* 3.1 7.5 + - - +
147A PHE* 3.0 21.8 + - - +
169A ILE* 4.0 9.3 - - - +
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Residues in contact with ASP 144 (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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88A LEU* 3.5 8.0 - - - +
140A GLN* 2.9 44.3 + - - +
141A LEU* 3.4 14.6 - - - +
143A ALA* 1.3 75.5 - - - +
145A GLY* 1.3 62.6 + - - +
147A PHE* 3.1 9.6 + - - +
148A VAL* 3.0 29.2 + - - +
1001A MBT 4.7 4.5 - - - -
145B GLY* 4.1 10.6 - - - +
152B ILE* 3.7 21.1 - - + +
153B HIS* 2.6 32.4 + - - -
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Residues in contact with GLY 145 (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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141A LEU 2.9 11.3 + - - -
142A ALA 3.1 1.9 + - - -
144A ASP* 1.3 78.0 - - - +
146A LEU* 1.3 60.1 + - - +
148A VAL* 3.8 4.1 - - - +
149A HIS* 3.0 25.6 + - - +
141B LEU* 3.4 30.7 - - - +
144B ASP* 4.0 10.6 - - - +
145B GLY* 4.0 8.2 - - - -
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Residues in contact with LEU 146 (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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85A VAL* 5.7 1.3 - - + +
88A LEU 3.8 2.2 - - - +
89A ALA* 3.8 28.5 - - + +
91A ASN* 3.6 0.3 - - - +
142A ALA 3.1 10.5 + - - +
143A ALA* 3.1 10.3 + - - +
145A GLY* 1.3 75.2 - - - +
147A PHE* 1.3 63.4 + - - +
148A VAL 3.3 0.5 + - - -
149A HIS* 3.4 10.5 + - + +
157A LEU* 3.6 31.0 - - + -
162A ARG* 2.9 53.0 + - + +
165A MET* 4.4 5.6 - - + -
166A LEU* 4.2 7.2 - - + +
169A ILE* 4.0 21.1 - - + -
141B LEU* 3.9 17.6 - - + +
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Residues in contact with PHE 147 (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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88A LEU* 3.2 32.3 + - + +
90A GLU 3.5 17.9 - - - -
91A ASN* 3.3 6.6 - - - -
92A VAL* 2.8 67.7 + - + +
96A GLU* 4.0 4.7 - - - -
100A LEU* 4.3 9.0 - - + -
143A ALA 3.0 10.2 + - - +
144A ASP* 3.1 12.1 + - - +
146A LEU* 1.3 76.6 - - - +
148A VAL* 1.3 69.3 + - + +
1001A MBT 3.1 61.5 - + - -
152B ILE* 4.6 7.9 - - + -
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Residues in contact with VAL 148 (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 ASN* 3.8 0.9 - - - -
92A VAL* 4.2 12.3 - - + -
97A LEU* 4.6 11.0 - - + -
144A ASP 3.0 19.2 + - - +
145A GLY* 3.8 7.0 - - - +
147A PHE* 1.3 92.2 - - + +
149A HIS* 1.3 67.9 + - - +
150A ASP 3.3 2.2 - - - -
151A TYR* 2.9 17.1 + - - +
152A ILE* 3.4 35.1 + - + +
144B ASP 4.8 0.4 - - - +
148B VAL* 3.9 21.1 - - + -
152B ILE* 4.2 23.1 - - + -
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Residues in contact with HIS 149 (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 ASN* 3.4 2.4 + - - -
145A GLY 3.0 15.7 + - - +
146A LEU* 3.4 12.8 + - - +
148A VAL* 1.3 77.2 - - - +
150A ASP* 1.3 70.5 + - - +
151A TYR 3.1 0.3 + - - -
152A ILE* 3.3 2.6 + - - -
153A HIS* 3.0 62.0 + + + +
155A ASP* 3.0 36.9 + - - -
157A LEU* 3.7 25.5 - - + +
162A ARG* 3.7 6.7 - - - +
137B TYR* 2.8 31.1 + + - -
141B LEU* 4.5 9.2 - - + -
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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