Contacts of the helix formed by residues 135 - 144 (chain A) in PDB entry 2VKM
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 PRO 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A SER* 3.6 26.2 - - - +
38A PHE 6.2 0.2 - - - +
120A GLY 4.6 3.4 - - - +
121A LEU 5.8 0.2 - - - -
122A ALA 3.8 11.7 - - - +
123A TYR 3.9 4.0 - - - -
124A ALA* 3.5 40.2 - - + +
127A ALA* 4.7 0.4 - - + -
133A LEU 3.5 6.5 - - - +
134A GLU* 1.3 88.1 - - + +
136A PHE* 1.3 66.2 + - - +
137A PHE* 3.4 4.0 - - + +
138A ASP* 3.2 29.1 + - - +
139A SER* 3.1 17.7 + - - -
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Residues in contact with PHE 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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18A MET* 3.9 16.2 - - + -
36A SER 4.9 0.6 + - - -
38A PHE* 4.3 23.5 - + + +
85A VAL* 3.9 23.6 - - + -
87A ILE* 4.2 17.9 - - + -
95A VAL* 3.9 26.7 - - + -
97A ALA* 3.6 21.1 - - + -
98A ASN 5.9 0.9 + - - +
119A LEU* 3.6 33.2 - - + -
120A GLY 4.7 5.3 + - - +
121A LEU* 5.0 0.4 - - + -
134A GLU 3.8 0.8 + - - -
135A PRO* 1.3 72.5 - - - +
137A PHE* 1.3 68.9 + + + +
139A SER* 3.1 8.2 + - - -
140A LEU* 2.9 47.5 + - + +
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Residues in contact with PHE 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LEU* 4.1 30.4 - - + +
122A ALA 6.0 0.2 - - - +
135A PRO* 3.4 3.0 - - + +
136A PHE* 1.3 84.2 - + - +
138A ASP* 1.3 62.4 + - - +
140A LEU* 3.3 27.1 + - + +
141A VAL* 3.0 30.5 + - + +
146A VAL* 5.0 0.4 - - + -
147A PRO 4.2 5.2 - - - -
148A ASN* 3.6 17.5 - - - -
149A LEU 3.7 29.8 - - - -
150A PHE* 3.9 18.6 - + + -
174A MET* 6.5 0.4 - - - -
176A ILE* 3.9 17.7 - - + -
347A ARG* 3.3 38.8 - - - +
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Residues in contact with ASP 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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122A ALA 4.7 1.6 - - - +
123A TYR* 5.0 4.6 - - - -
124A ALA* 4.7 4.9 + - - -
134A GLU* 3.8 16.4 - - + -
135A PRO* 3.2 34.7 + - + +
136A PHE 3.2 0.4 - - - -
137A PHE* 1.3 75.1 - - - +
139A SER* 1.3 65.1 + - - +
141A VAL* 3.4 5.3 + - - +
142A LYS* 3.0 42.1 + - - +
347A ARG* 3.3 25.6 + - - +
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Residues in contact with SER 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A VAL* 4.5 6.3 - - - -
96A ARG 4.0 10.5 + - - -
97A ALA* 4.5 7.4 - - - +
98A ASN* 4.9 1.6 + - - -
134A GLU* 2.6 37.6 + - - +
135A PRO 3.1 5.5 + - - -
136A PHE* 3.1 11.9 + - - -
138A ASP* 1.3 77.7 - - - +
140A LEU* 1.3 57.6 + - - +
142A LYS* 3.3 1.5 + - - +
143A GLN* 2.9 51.2 + - - +
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Residues in contact with LEU 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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87A ILE* 5.4 4.0 - - + -
91A PRO* 5.0 2.7 - - + -
93A VAL* 3.9 16.6 - - + -
95A VAL* 3.6 29.1 - - + +
136A PHE* 2.9 31.1 + - + +
137A PHE* 3.4 39.0 - - + +
138A ASP 3.2 0.2 - - - -
139A SER* 1.3 77.7 - - - +
141A VAL* 1.3 59.5 + - + +
144A THR* 2.7 46.0 + - - +
146A VAL* 4.4 10.1 - - + -
176A ILE* 3.8 19.3 - - + -
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Residues in contact with VAL 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 PHE* 3.0 35.1 + - + +
138A ASP* 4.0 5.6 - - - +
140A LEU* 1.3 77.8 - - + +
142A LYS* 1.3 61.7 + - + +
144A THR* 2.7 24.7 - - - +
146A VAL* 4.1 17.9 - - + +
147A PRO 4.4 0.2 - - - +
148A ASN* 3.4 44.2 - - + +
347A ARG* 5.6 0.2 - - - +
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Residues in contact with LYS 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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134A GLU* 2.7 37.6 + - - +
138A ASP* 3.0 31.6 + - - +
139A SER* 3.7 4.3 - - - +
141A VAL* 1.3 81.7 - - + +
143A GLN* 1.3 63.4 + - + +
144A THR 3.7 1.4 + - - +
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Residues in contact with GLN 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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94A THR 4.5 1.9 - - - +
95A VAL* 3.3 11.2 - - + -
96A ARG* 2.8 50.5 + - - +
134A GLU* 4.7 3.8 + - - -
139A SER* 2.9 30.7 + - - +
140A LEU 4.4 1.3 - - - +
142A LYS* 1.3 79.3 - - + +
144A THR* 1.3 67.9 + - + +
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Residues in contact with THR 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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93A VAL* 3.7 39.0 - - + -
94A THR 4.6 4.3 - - - +
95A VAL* 4.3 9.2 - - + -
140A LEU* 2.7 25.4 + - + +
141A VAL 2.7 17.5 - - - +
142A LYS 4.4 1.4 - - - +
143A GLN* 1.3 85.9 - - + +
145A HIS* 1.3 70.8 + - - +
146A VAL* 3.2 22.4 + - - +
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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