Contacts of the helix formed by residues 115 - 126 (chain A) in PDB entry 5VEY
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 115 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A TYR* 3.5 32.8 - - + +
16A TYR* 3.7 29.4 - - + +
107A SER* 4.7 7.0 - - - -
113A GLN 3.6 1.0 - - - +
114A PHE* 1.3 78.4 - - + +
116A VAL* 1.3 63.8 + - - +
117A GLY 3.3 2.0 - - - +
118A ARG* 3.6 31.2 - - + +
119A VAL* 3.2 24.9 + - - +
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Residues in contact with VAL 116 (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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106A ARG* 4.1 15.9 - - + +
107A SER* 3.6 29.5 - - - +
110A ALA* 4.0 4.0 - - + -
112A LEU* 3.7 31.9 - - + -
114A PHE 2.9 15.3 + - - +
115A PRO* 1.3 71.5 - - - +
117A GLY* 1.3 63.7 + - - +
119A VAL* 3.2 18.8 + - - +
120A HIS* 3.3 9.4 + - - +
137A PRO* 3.8 6.0 - - + +
138A VAL* 3.5 37.0 - - + +
141A ALA* 4.3 4.3 - - + -
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Residues in contact with GLY 117 (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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106A ARG* 4.2 26.7 - - - +
107A SER* 4.8 1.8 - - - +
115A PRO* 3.3 1.0 - - - +
116A VAL* 1.3 78.5 - - - +
118A ARG* 1.3 62.0 + - - +
120A HIS* 3.3 6.4 + - - +
121A ARG* 2.9 41.9 + - - +
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Residues in contact with ARG 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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11A GLU* 3.9 21.6 - - - +
12A SER 6.0 1.3 - - - +
13A TYR* 3.6 21.3 - - - +
115A PRO* 3.3 31.7 + - + +
116A VAL 3.2 0.8 - - - -
117A GLY* 1.3 72.5 - - - +
119A VAL* 1.3 65.3 + - - +
121A ARG* 3.2 16.6 + - + +
122A LEU* 3.0 38.6 + - + +
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Residues in contact with VAL 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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13A TYR* 4.9 10.5 - - + +
46A PHE* 3.8 21.1 - - + -
114A PHE* 5.6 4.5 - - + -
115A PRO 3.2 18.2 - - - +
116A VAL* 3.2 10.3 + - - +
118A ARG* 1.3 76.5 - - - +
120A HIS* 1.3 62.8 + - - +
122A LEU* 3.1 12.7 + - + +
123A LEU* 3.1 24.4 + - + +
137A PRO* 3.8 26.2 - - + +
140A LEU* 4.0 12.6 - - + -
141A ALA* 4.4 14.1 - - + +
144A LEU* 5.1 8.1 - - + -
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Residues in contact with HIS 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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106A ARG* 5.2 13.6 + - - -
116A VAL 3.3 4.4 + - - +
117A GLY* 3.3 12.5 + - - +
119A VAL* 1.3 80.4 - - - +
121A ARG* 1.3 65.1 + - + +
123A LEU* 3.4 5.3 + - - +
124A ARG* 3.4 36.4 + - - +
132A VAL* 2.8 38.6 + - + +
133A GLY 3.0 22.6 + - - -
134A ALA* 4.3 6.6 - - + +
137A PRO* 3.4 20.9 - - + +
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Residues in contact with ARG 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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106A ARG* 4.6 14.6 - - - +
117A GLY* 2.9 37.6 + - - +
118A ARG* 3.2 16.6 + - + +
120A HIS* 1.3 78.4 - - + +
122A LEU* 1.3 60.0 + - + +
124A ARG* 3.3 7.2 + - - +
125A LYS* 2.9 53.3 + - - +
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Residues in contact with LEU 122 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A LYS* 5.4 11.2 - - + +
11A GLU* 3.4 28.7 - - + +
13A TYR* 4.1 10.1 - - - +
46A PHE* 3.5 31.4 - - + -
118A ARG* 3.0 38.8 + - + +
119A VAL* 3.1 12.3 + - + +
121A ARG* 1.3 77.1 - - + +
123A LEU* 1.3 57.9 + - - +
125A LYS* 3.7 15.6 - - + +
126A GLY* 2.9 27.0 + - - -
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Residues in contact with LEU 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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46A PHE* 3.4 23.8 - - + -
50A ALA* 4.4 19.3 - - + -
53A ALA* 6.4 0.7 - - + -
65A ILE* 5.6 12.3 - - + -
70A ILE* 5.7 3.4 - - + -
119A VAL* 3.1 18.7 + - + +
120A HIS* 3.6 5.6 - - - +
121A ARG 3.3 0.2 - - - -
122A LEU* 1.3 78.5 - - - +
124A ARG* 1.3 61.4 + - - +
126A GLY 3.5 5.4 + - - -
127A ASN 3.8 5.4 + - - -
128A TYR* 3.8 21.2 + - + +
129A SER 4.7 1.0 + - - -
132A VAL* 3.6 35.7 - - + +
136A ALA* 4.9 4.7 - - + -
137A PRO* 4.0 23.6 - - + -
140A LEU* 4.7 7.9 - - + -
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Residues in contact with ARG 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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120A HIS* 3.4 31.3 + - - +
121A ARG* 3.3 9.5 + - - +
122A LEU 3.3 0.2 - - - -
123A LEU* 1.3 73.4 - - - +
125A LYS* 1.3 67.2 + - + +
127A ASN* 3.0 15.2 + - - +
129A SER 4.6 10.1 - - - +
130A GLU 3.3 25.1 + - - +
131A ARG* 3.6 17.4 - - - +
132A VAL* 3.3 25.8 + - + +
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Residues in contact with LYS 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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10A LYS* 6.1 2.7 - - - +
121A ARG* 2.9 43.2 + - - +
122A LEU* 3.3 17.9 + - + +
124A ARG* 1.3 71.7 - - + +
126A GLY* 1.3 58.4 + - - +
127A ASN* 2.9 14.5 + - - +
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Residues in contact with GLY 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 LEU 2.9 13.6 + - - -
124A ARG 3.2 0.8 - - - -
125A LYS* 1.3 75.3 - - - +
127A ASN* 1.3 68.9 + - - +
128A TYR* 3.0 35.2 + - - -
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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