Contacts of the helix formed by residues 117 - 131 (chain A) in PDB entry 1VE3
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 GLU 117 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116A PHE* 1.3 75.5 - - - +
118A PRO* 1.3 76.8 - - + +
119A LEU* 3.9 28.7 - - + +
120A GLU* 2.9 35.5 + - + +
121A LEU* 2.9 18.5 + - - +
192A ASN* 3.4 19.2 - - - +
194A TRP* 3.8 0.9 - - - -
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Residues in contact with PRO 118 (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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117A GLU* 1.3 89.4 - - + +
119A LEU* 1.3 57.6 + - - +
121A LEU 3.3 0.5 + - - -
122A ASN* 2.9 29.7 + - - +
173A GLU 5.8 1.1 - - - +
174A ARG* 3.7 36.6 - - + +
192A ASN* 5.0 1.8 - - + +
194A TRP* 3.6 24.8 - - + -
202A LEU* 3.8 10.7 - - + +
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Residues in contact with LEU 119 (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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117A GLU* 3.9 20.4 - - - +
118A PRO* 1.3 79.5 - - - +
120A GLU* 1.3 81.6 + - + +
122A ASN* 3.6 9.3 - - - +
123A GLN* 2.9 42.1 + - - +
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Residues in contact with GLU 120 (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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95A ARG* 3.4 34.6 + - - +
115A HIS 3.5 7.4 - - - +
116A PHE* 3.4 17.4 - - + -
117A GLU* 2.9 41.6 + - + +
119A LEU* 1.3 90.9 - - + +
121A LEU* 1.3 67.4 + - - +
122A ASN 3.1 1.3 - - - -
123A GLN* 3.1 16.2 + - - +
124A VAL* 3.0 25.1 + - - +
192A ASN* 4.8 0.7 + - - -
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Residues in contact with LEU 121 (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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109A PHE* 4.0 24.0 - - + -
113A ILE* 4.3 15.5 - - + -
116A PHE* 3.8 14.7 - - + +
117A GLU 2.9 14.7 + - - +
118A PRO 3.9 2.0 - - - +
120A GLU* 1.3 77.5 - - - +
122A ASN* 1.3 62.7 + - - +
124A VAL* 3.3 6.9 + - + -
125A PHE* 3.0 61.1 + - + -
194A TRP* 3.5 42.6 - - + +
199A VAL* 4.9 6.3 - - + -
202A LEU* 4.4 3.6 - - + -
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Residues in contact with ASN 122 (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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118A PRO 2.9 17.9 + - - +
119A LEU* 3.6 11.7 - - - +
120A GLU 3.1 0.2 - - - -
121A LEU* 1.3 78.4 - - - +
123A GLN* 1.3 62.9 + - - +
125A PHE* 3.5 3.8 + - - -
126A LYS* 3.1 32.6 + - - +
202A LEU* 4.4 16.9 - - + +
205A LEU* 4.2 11.7 - - - +
206A TYR* 2.5 40.6 + - - -
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Residues in contact with GLN 123 (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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95A ARG* 3.4 37.9 + - + +
119A LEU* 2.9 33.6 + - - +
120A GLU* 3.1 20.0 + - - +
122A ASN* 1.3 77.7 - - + +
124A VAL* 1.3 59.8 + - - +
126A LYS* 3.3 10.0 + - - +
127A GLU* 2.9 31.7 + - - +
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Residues in contact with VAL 124 (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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45A LEU* 3.8 26.5 - - + -
94A ALA* 3.7 20.2 - - + +
95A ARG* 3.8 6.3 - - + -
109A PHE* 4.5 17.0 - - + -
116A PHE* 3.5 31.6 - - + -
120A GLU 3.0 14.6 + - - +
121A LEU* 3.3 10.3 + - + +
123A GLN* 1.3 76.8 - - - +
125A PHE* 1.3 63.4 + - + +
127A GLU* 3.1 3.6 + - - +
128A VAL* 2.8 37.6 + - + +
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Residues in contact with PHE 125 (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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109A PHE* 4.7 2.5 - + - -
121A LEU* 3.0 47.0 + - + +
122A ASN* 3.8 2.7 - - - +
124A VAL* 1.3 79.1 - - + +
126A LYS* 1.3 61.2 + - - +
128A VAL* 3.3 5.3 + - - +
129A ARG* 3.0 21.7 + - - +
138A PHE* 3.6 33.9 - + - -
140A MSE 3.8 21.5 - - - -
199A VAL* 3.7 15.5 - - + -
202A LEU* 3.8 16.8 - - + -
203A ALA* 3.7 37.2 - - + -
206A TYR* 3.5 18.3 - + + -
207A PHE* 3.6 12.4 - + + -
224A TYR* 5.9 0.7 - + - -
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Residues in contact with LYS 126 (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 ASN* 3.1 24.2 + - - +
123A GLN* 3.5 12.7 - - - +
124A VAL 3.2 0.2 - - - -
125A PHE* 1.3 77.5 - - - +
127A GLU* 1.3 64.1 + - + +
129A ARG* 3.4 4.8 + - - +
130A ARG* 3.1 21.5 + - - +
206A TYR* 3.0 43.7 + - + -
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Residues in contact with GLU 127 (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 ALA 3.8 11.0 - - - +
95A ARG 3.4 28.5 - - - +
96A LYS* 3.9 14.0 - - + +
97A LEU* 2.8 33.7 + - + +
123A GLN 2.9 12.9 + - - +
124A VAL 3.5 3.6 - - - +
126A LYS* 1.3 76.0 - - + +
128A VAL* 1.3 64.7 + - - +
130A ARG* 2.9 46.6 + - - +
131A VAL* 3.1 28.8 + - - +
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Residues in contact with VAL 128 (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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45A LEU* 3.8 27.4 - - + -
97A LEU* 5.4 0.7 - - + -
107A VAL* 3.9 16.8 - - + -
124A VAL* 2.8 31.7 + - + +
125A PHE* 3.3 6.9 + - - +
127A GLU* 1.3 69.9 - - + +
129A ARG* 1.3 66.6 + - - +
131A VAL* 3.4 8.9 + - - +
132A LEU* 3.1 28.7 + - + +
138A PHE* 3.5 47.1 - - + -
207A PHE* 3.9 8.5 - - + -
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Residues in contact with ARG 129 (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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125A PHE 3.0 16.7 + - - +
126A LYS* 3.7 5.7 + - - +
128A VAL* 1.3 77.9 - - - +
130A ARG* 1.3 71.4 + - - +
132A LEU* 3.3 20.5 + - - +
206A TYR* 3.6 35.4 - - + +
207A PHE* 4.0 17.0 - - + -
226A PRO* 4.0 12.6 - - + +
227A LYS* 2.7 40.2 + - - +
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Residues in contact with ARG 130 (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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96A LYS* 4.5 4.9 - - - +
97A LEU 3.0 17.4 + - - -
98A SER 4.8 0.2 - - - -
99A PHE 3.0 24.9 + - - -
100A GLU* 3.6 3.0 + - - +
101A ASP* 2.6 57.2 + - + +
102A LYS* 2.8 24.9 + - - +
126A LYS 3.1 11.2 + - - +
127A GLU* 2.9 46.5 + - - +
128A VAL 3.2 0.4 - - - -
129A ARG* 1.3 92.2 - - - +
131A VAL* 1.3 70.2 + - - +
132A LEU 3.2 1.8 + - - +
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Residues in contact with VAL 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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43A LEU* 4.4 6.5 - - + -
97A LEU* 4.2 21.3 - - + -
99A PHE* 4.1 11.9 - - + -
100A GLU 3.9 9.9 - - - +
102A LYS 3.8 4.9 - - - +
103A THR 2.7 23.8 + - - -
104A PHE* 2.8 31.9 + - + -
107A VAL* 4.4 4.7 - - + -
127A GLU 3.1 17.9 + - - +
128A VAL* 3.4 11.9 - - - +
130A ARG* 1.3 102.3 - - - +
132A LEU* 1.3 58.6 + - - +
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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