Contacts of the helix formed by residues 115 - 130 (chain A) in PDB entry 4PIM
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 115 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A ALA* 6.0 2.6 - - - +
113A ASP* 3.0 13.9 + - - +
114A VAL* 1.3 81.2 - - + +
116A ALA* 1.3 63.4 + - - +
117A GLY* 2.9 18.4 + - - -
118A VAL* 3.1 28.7 + - + +
119A LEU* 3.1 23.0 + - - +
139A CYS* 4.4 1.3 - - - -
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Residues in contact with ALA 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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5A LEU* 4.3 15.4 - - + +
7A ASN* 3.8 25.6 - - - +
114A VAL 4.0 0.2 + - - -
115A ASP* 1.3 72.4 + - - +
117A GLY* 1.3 57.8 + - - +
119A LEU* 3.1 14.7 + - - +
120A ARG* 2.9 37.1 + - - +
139A CYS* 3.8 8.7 - - + -
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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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115A ASP* 2.9 9.2 + - - -
116A ALA* 1.3 78.7 - - - +
118A VAL* 1.3 60.3 + - - +
120A ARG* 3.4 10.7 + - - +
121A SER* 3.1 26.9 + - - -
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Residues in contact with VAL 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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87A SER* 4.6 24.0 - - - +
89A THR* 5.4 10.1 - - + -
113A ASP* 4.4 9.9 - - + +
115A ASP* 3.1 34.1 + - + +
117A GLY* 1.3 72.8 - - - +
119A LEU* 1.3 62.8 + - - +
121A SER* 3.2 8.4 + - - -
122A ALA* 2.9 27.9 + - + +
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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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3A LEU* 4.9 3.4 - - - +
5A LEU* 3.9 11.7 - - + -
87A SER 4.1 4.9 - - - +
111A PRO* 3.7 42.2 - - + +
113A ASP* 3.7 26.5 - - + +
115A ASP 3.1 13.4 + - - +
116A ALA* 3.1 7.8 + - - +
118A VAL* 1.3 76.8 - - - +
120A ARG* 1.3 56.1 + - - +
122A ALA* 3.2 5.0 + - - +
123A GLY* 2.9 27.5 + - - -
137A ALA* 4.2 11.2 - - + -
138A VAL 3.5 24.5 - - - +
139A CYS* 3.7 23.3 - - + +
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Residues in contact with ARG 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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3A LEU* 4.1 29.6 - - + +
5A LEU* 3.6 26.6 - - + +
116A ALA* 2.9 22.7 + - - +
117A GLY* 3.7 11.2 - - - +
119A LEU* 1.3 75.4 - - - +
121A SER* 1.3 64.4 + - - +
123A GLY* 3.4 1.4 + - - -
124A ALA* 3.1 23.2 + - - +
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Residues in contact with SER 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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117A GLY 3.1 14.6 + - - -
118A VAL* 3.6 11.3 - - - -
120A ARG* 1.3 75.6 - - - +
122A ALA* 1.3 61.6 + - - +
124A ALA* 3.3 7.0 + - - +
125A ALA* 3.0 24.5 + - - +
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Residues in contact with ALA 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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87A SER 4.1 19.7 - - - +
88A GLY* 4.2 21.1 - - - +
89A THR* 5.5 2.2 - - - +
109A PHE* 4.8 8.3 - - + -
111A PRO* 5.1 2.7 - - + -
118A VAL* 2.9 17.9 + - + +
119A LEU* 3.5 6.3 - - - +
121A SER* 1.3 74.5 - - - +
123A GLY* 1.3 65.3 + - - +
125A ALA* 3.3 4.4 + - - +
126A ILE* 2.9 32.1 + - - +
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Residues in contact with GLY 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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0A HIS 4.6 2.8 - - - +
2A ALA 4.9 3.8 - - - +
3A LEU* 4.2 9.6 - - - -
109A PHE* 5.6 0.2 - - - -
111A PRO* 5.7 0.6 - - - +
119A LEU 2.9 16.0 + - - -
120A ARG 3.8 1.8 - - - -
122A ALA* 1.3 76.5 - - - +
124A ALA* 1.3 57.6 + - - +
127A GLY* 2.9 27.0 + - - -
135A ILE* 3.2 33.7 - - - +
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Residues in contact with ALA 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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0A HIS* 3.4 30.4 + - - +
120A ARG 3.1 13.7 + - - +
121A SER* 3.6 9.4 - - - +
123A GLY* 1.3 76.6 - - - +
125A ALA* 1.3 62.2 + - - +
127A GLY 4.1 0.3 - - - -
128A ALA* 3.2 24.4 + - - +
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Residues in contact with ALA 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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88A GLY 6.1 0.2 - - - +
94A ARG* 3.4 23.4 + - - +
121A SER 3.0 17.4 + - - +
122A ALA* 3.9 5.6 - - - +
124A ALA* 1.3 75.9 - - - +
126A ILE* 1.3 64.5 + - + +
128A ALA* 3.4 6.4 + - - +
129A GLU* 3.1 23.4 + - - +
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Residues in contact with ILE 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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88A GLY 4.2 16.4 - - - +
93A THR* 5.0 1.1 - - + -
94A ARG* 4.0 30.3 - - + +
97A LEU* 3.8 24.5 - - + -
109A PHE* 3.9 32.8 - - + -
122A ALA* 2.9 21.8 + - - +
125A ALA* 1.3 72.2 - - + +
127A GLY* 1.3 65.4 + - - +
129A GLU* 4.5 0.2 - - - -
130A TYR* 3.0 43.8 + - + +
133A ILE* 3.9 13.6 - - + +
135A ILE* 4.2 6.5 - - + -
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Residues in contact with GLY 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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0A HIS 4.8 9.2 - - - -
2A ALA 6.1 0.2 - - - -
123A GLY 2.9 20.5 + - - -
124A ALA 4.1 0.4 - - - -
126A ILE* 1.3 77.6 - - - +
128A ALA* 1.3 61.3 + - - +
130A TYR 3.7 14.6 - - - +
131A PRO* 3.7 7.6 - - - +
132A GLY 4.7 0.9 + - - -
133A ILE* 4.0 8.5 - - - +
135A ILE* 3.6 12.2 - - - +
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Residues in contact with ALA 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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0A HIS* 4.6 9.3 - - - +
124A ALA 3.2 18.9 + - - +
125A ALA* 3.6 6.5 - - - +
126A ILE 3.2 0.2 - - - -
127A GLY* 1.3 79.3 - - - +
129A GLU* 1.3 60.1 + - - +
130A TYR 3.6 0.3 + - - -
131A PRO* 3.8 12.3 - - - +
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Residues in contact with GLU 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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94A ARG* 3.7 19.7 + - - +
101A ARG* 2.9 44.0 + - - -
125A ALA 3.1 15.7 + - - +
128A ALA* 1.3 78.9 - - - +
130A TYR* 1.3 90.5 + - + +
131A PRO* 3.3 6.3 - - - +
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Residues in contact with TYR 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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94A ARG* 3.6 17.6 + - - +
97A LEU* 3.5 40.3 - - + +
98A ASP* 2.6 21.5 + - - -
101A ARG* 3.3 43.7 - - - +
106A LEU* 3.8 18.8 - - + -
126A ILE* 3.0 34.6 + - + +
127A GLY 3.7 3.7 - - - +
129A GLU* 1.3 96.4 - - + +
131A PRO* 1.3 68.8 - - - +
132A GLY 3.2 0.2 + - - -
133A ILE* 3.0 35.7 + - + +
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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