Contacts of the helix formed by residues 117 - 135 (chain A) in PDB entry 4P8V
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 SER 117 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A VAL 3.2 0.2 + - - -
116A ASP* 1.3 81.4 - - - +
118A SER* 1.3 58.3 + - - +
119A THR* 3.4 12.2 + - - -
120A SER* 3.1 23.2 + - - -
121A ARG* 3.0 36.1 + - - +
404A SO4 3.5 13.5 - - - -
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Residues in contact with SER 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A SER* 1.3 74.2 - - - +
119A THR* 1.3 62.7 + - - +
121A ARG* 3.3 25.4 - - - +
122A LEU* 2.9 30.1 + - - +
161A GLU* 4.5 7.8 - - - +
404A SO4 3.2 16.8 + - - -
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Residues in contact with THR 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A SER* 3.2 9.7 + - - -
118A SER* 1.3 80.9 + - - +
120A SER* 1.3 60.4 + - - +
122A LEU* 3.4 8.1 + - + +
123A GLU* 3.1 29.6 + - + +
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Residues in contact with SER 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ASN* 3.7 32.3 - - - +
113A PRO 3.5 6.2 + - - -
114A MET* 2.6 25.2 + - - +
116A ASP* 4.7 0.7 - - - +
117A SER* 3.1 24.9 + - - -
119A THR* 1.3 78.5 - - - +
121A ARG* 1.3 61.6 + - - +
123A GLU* 3.4 9.4 + - - +
124A PHE* 3.2 20.6 + - - +
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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
----------------------------------------------------------
114A MET* 3.5 26.0 - - - +
115A VAL* 2.9 39.9 + - - +
117A SER 3.0 18.5 + - - +
118A SER* 3.3 17.2 - - - +
120A SER* 1.3 74.5 + - - +
122A LEU* 1.3 60.8 + - - +
124A PHE* 3.2 1.9 + - - +
125A ILE* 2.9 38.7 + - + +
154A HIS* 4.6 7.7 - - - -
157A VAL* 3.5 16.2 - - - +
158A LEU* 4.3 24.7 - - + +
161A GLU* 2.7 45.5 + - - +
404A SO4 2.9 40.0 + - - -
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Residues in contact with LEU 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 SER 2.9 20.2 + - - +
119A THR* 3.6 7.9 - - + +
120A SER 3.3 0.2 - - - -
121A ARG* 1.3 73.0 - - - +
123A GLU* 1.3 67.5 + - - +
125A ILE* 4.4 12.3 - - + +
126A ASN* 3.0 48.7 + - - +
161A GLU* 5.2 0.2 + - - -
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Residues in contact with GLU 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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68A ASN 3.4 13.7 - - - +
69A ASN* 3.2 34.3 + - - +
70A LYS* 3.8 25.2 + - + +
119A THR* 3.1 15.1 + - + +
120A SER* 3.4 12.2 - - - +
122A LEU* 1.3 74.5 - - - +
124A PHE* 1.3 63.1 + - - +
126A ASN* 3.5 5.3 + - - +
127A SER* 3.0 23.6 + - - -
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Residues in contact with PHE 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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66A ILE* 3.8 27.6 - - + -
69A ASN 3.0 24.2 + - - +
71A VAL* 4.1 14.6 - - + -
101A ILE* 3.4 29.8 - - + -
111A PHE* 6.0 1.1 - + - -
114A MET* 3.6 41.5 - - + -
120A SER 3.2 1.8 + - - +
121A ARG 3.4 7.9 - - - +
123A GLU* 1.3 82.4 - - - +
125A ILE* 1.3 61.6 + - + +
127A SER* 2.6 23.1 + - - -
128A ILE* 2.9 33.6 + - + +
140A LEU* 5.0 4.0 - - + -
142A VAL* 6.3 0.9 - - + -
158A LEU* 4.3 14.6 - - + -
162A LEU* 4.9 7.9 - - + -
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Residues in contact with ILE 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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121A ARG* 2.9 28.4 + - + +
122A LEU* 3.3 12.1 + - + +
124A PHE* 1.3 79.1 - - + +
126A ASN* 1.3 68.1 + - - +
128A ILE* 3.2 7.9 + - - +
129A ILE* 3.1 28.3 + - + +
158A LEU* 4.7 5.2 - - + +
161A GLU* 3.5 45.1 - - + +
162A LEU* 3.8 26.5 - - + +
165A ALA* 3.4 30.7 - - + -
166A PHE* 5.2 0.4 - - + -
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Residues in contact with ASN 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* 3.0 46.6 + - - +
123A GLU* 3.9 5.3 - - - +
125A ILE* 1.3 80.5 - - - +
127A SER* 1.3 61.7 + - - +
129A ILE* 3.4 11.4 + - - +
130A LEU* 3.2 23.2 + - - +
165A ALA* 5.7 0.9 - - - +
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Residues in contact with SER 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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70A LYS* 3.4 31.1 - - - -
71A VAL* 3.1 26.0 + - - +
123A GLU 3.0 14.8 + - - -
124A PHE* 2.6 18.8 + - - -
126A ASN* 1.3 77.2 - - - +
128A ILE* 1.3 53.9 + - - +
130A LEU* 3.5 7.6 + - - +
131A PHE* 2.9 31.5 + - - +
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Residues in contact with ILE 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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71A VAL* 3.5 33.2 - - + -
99A LEU* 5.2 2.2 - - + -
101A ILE* 3.9 7.6 - - + -
124A PHE* 2.9 45.3 + - + +
125A ILE* 3.2 10.1 + - - +
127A SER* 1.3 75.3 + - - +
129A ILE* 1.3 67.7 + - - +
131A PHE* 4.5 0.2 - - - -
132A LEU* 2.9 50.4 + - + +
140A LEU* 3.9 18.4 - - + -
162A LEU* 4.5 1.8 - - + -
166A PHE* 3.7 22.7 - - + -
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Residues in contact with ILE 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 ILE* 3.1 18.0 + - + +
126A ASN* 4.0 12.1 - - - +
127A SER 3.4 0.2 - - - -
128A ILE* 1.3 74.9 - - - +
130A LEU* 1.3 63.1 + - - +
132A LEU* 4.1 0.7 - - - +
133A ARG* 3.1 35.2 + - + +
165A ALA* 3.8 36.6 - - + +
166A PHE* 3.8 21.5 - - + -
169A ASP* 3.7 31.6 - - + +
178A LEU* 4.2 12.8 - - + -
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Residues in contact with LEU 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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126A ASN 3.2 16.8 + - - +
127A SER* 3.8 6.5 - - - +
129A ILE* 1.3 79.3 - - - +
131A PHE* 1.3 58.5 + - - +
133A ARG* 3.8 3.4 - - + +
134A ASN* 2.8 66.5 + - - +
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Residues in contact with PHE 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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71A VAL* 3.5 30.5 - - + -
72A ILE* 4.4 7.6 - - + -
73A ILE* 3.7 24.2 - - + -
78A GLU* 4.6 3.6 - - - -
82A TYR* 3.2 22.9 - - - -
99A LEU* 3.7 31.9 - - + -
127A SER 2.9 19.3 + - - +
128A ILE 3.3 1.8 + - - +
130A LEU* 1.3 79.1 - - - +
132A LEU* 1.3 66.3 + - + +
134A ASN* 4.5 2.2 - - - +
135A HIS* 3.0 50.3 + + - +
137A PHE* 4.0 11.2 - + - -
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Residues in contact with LEU 132 (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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99A LEU* 3.8 28.3 - - + -
128A ILE* 2.9 41.9 + - + +
129A ILE 4.2 1.8 - - - +
131A PHE* 1.3 78.4 - - + +
133A ARG* 1.3 63.3 + - - +
136A ASN 3.1 4.2 + - - -
137A PHE* 2.9 55.3 + - + +
139A GLY* 3.7 35.2 - - - +
140A LEU* 4.0 6.1 - - + +
166A PHE* 4.4 1.8 - - + -
178A LEU* 4.1 24.0 - - + -
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Residues in contact with ARG 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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129A ILE* 3.1 26.2 + - + +
130A LEU* 4.0 4.3 - - + +
132A LEU* 1.3 73.8 - - - +
134A ASN* 1.3 67.6 + - - +
135A HIS 3.2 0.7 + - - -
136A ASN* 3.5 9.1 + - - +
137A PHE 5.1 4.3 + - - -
138A ASP* 6.1 0.2 - - - +
169A ASP* 3.0 28.9 + - - +
170A PHE 5.4 0.2 - - - +
173A SER* 3.9 14.7 + - - -
175A LYS* 3.7 50.2 + - - +
176A GLU* 2.9 30.9 + - - +
177A ARG* 4.6 1.4 - - - +
178A LEU* 3.8 30.6 - - + +
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Residues in contact with ASN 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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130A LEU* 2.8 52.8 + - - +
131A PHE* 3.9 4.6 - - - +
133A ARG* 1.3 74.7 - - - +
135A HIS* 1.3 76.1 + - + +
136A ASN* 3.7 1.4 + - - +
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Residues in contact with HIS 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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78A GLU* 5.2 0.6 + - - -
82A TYR* 3.5 47.6 + + + +
85A ILE* 4.0 11.8 - - - +
86A ASN* 4.7 1.3 - - - +
131A PHE* 3.0 54.9 + + - +
133A ARG 3.1 0.2 - - - -
134A ASN* 1.3 92.6 + - + +
136A ASN* 1.3 69.6 + - - +
137A PHE* 3.3 24.9 + - + -
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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
------------------------------------------------------------
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