Contacts of the helix formed by residues 116 - 128 (chain A) in PDB entry 4MYF
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 GLN 116 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A PHE* 3.5 28.8 - - + +
93A LEU* 3.8 11.6 - - + +
109A VAL* 3.4 21.4 + - - +
111A GLY* 3.4 21.3 - - - +
113A GLY 3.2 16.3 + - - +
114A ASN 3.0 1.0 + - - -
115A ASP* 1.3 78.2 - - - +
117A SER* 1.3 64.3 + - - +
118A ALA 3.2 0.2 - - - -
119A PRO* 3.1 14.7 - - - +
120A ASN* 3.2 17.8 + - - +
270A ASP* 3.6 13.0 - - - +
271A MET 3.2 31.3 + - - +
272A SER* 2.8 23.7 + - - +
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Residues in contact with SER 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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114A ASN* 3.0 15.9 + - - -
116A GLN* 1.3 77.6 - - - +
118A ALA* 1.3 57.2 + - - +
120A ASN* 3.8 3.4 - - - -
121A GLY 2.8 23.6 + - - -
157A PRO* 4.0 4.0 - - - -
158A PHE* 3.7 28.4 - - - -
161A LEU* 3.6 6.3 - - - +
224A PHE* 3.5 8.2 - - - -
226A SER* 3.2 11.2 + - - -
270A ASP* 2.9 24.8 + - - -
272A SER* 3.9 7.3 + - - -
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Residues in contact with ALA 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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115A ASP 3.3 5.6 + - - +
117A SER* 1.3 75.4 - - - +
119A PRO* 1.4 68.7 - - + +
121A GLY 3.3 1.7 + - - -
122A ARG* 2.9 33.0 + - - +
157A PRO* 3.6 23.0 - - + +
160A GLN* 3.6 39.7 - - + +
161A LEU* 3.4 10.6 - - - +
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Residues in contact with PRO 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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90A HIS* 3.4 56.1 - - + +
93A LEU* 4.2 7.0 - - + -
94A GLU* 3.4 25.6 - - + +
115A ASP 3.2 10.5 - - - +
116A GLN 3.1 13.0 - - - +
118A ALA* 1.4 93.9 - - + +
120A ASN* 1.3 62.0 + - - +
122A ARG* 3.2 17.5 + - - +
123A ALA* 3.0 18.9 + - - +
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Residues in contact with ASN 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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93A LEU* 3.5 12.4 - - - +
97A VAL* 3.3 23.1 - - - +
109A VAL* 3.7 12.0 - - - +
116A GLN* 3.2 21.5 + - - +
117A SER 3.8 0.9 - - - +
119A PRO* 1.3 80.0 - - - +
121A GLY* 1.3 61.0 + - - +
123A ALA* 3.3 8.8 + - - +
124A MET* 3.2 23.6 + - - +
224A PHE* 3.7 13.0 - - + -
268A MET* 3.7 23.3 - - + +
270A ASP* 2.9 34.2 + - - +
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Residues in contact with GLY 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 SER 2.8 20.3 + - - -
120A ASN* 1.3 72.2 - - - +
122A ARG* 1.3 58.3 + - - +
124A MET* 3.1 9.1 + - - +
125A LEU* 2.9 30.5 + - - +
132A VAL* 5.3 0.2 - - - +
134A VAL* 5.6 2.7 - - - -
161A LEU* 3.7 22.4 - - - -
224A PHE* 3.7 13.4 - - - -
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Residues in contact with ARG 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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90A HIS* 4.7 9.5 + - - +
94A GLU* 2.9 34.0 + - - +
118A ALA* 2.9 20.5 + - - +
119A PRO* 3.2 32.6 + - - +
121A GLY* 1.3 77.6 - - - +
123A ALA* 1.3 62.1 + - - +
125A LEU* 3.1 7.2 + - - +
126A ARG* 3.0 30.1 + - - -
160A GLN* 3.0 35.2 - - - +
161A LEU* 3.7 7.3 - - + +
164A GLU* 3.7 27.1 + - - +
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Residues in contact with ALA 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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94A GLU* 3.4 30.4 - - - +
97A VAL* 3.7 13.7 - - + -
98A PHE* 3.6 24.0 - - - +
101A LEU* 3.9 2.4 - - - +
119A PRO 3.0 10.7 + - - +
120A ASN 3.5 9.0 - - - +
121A GLY 3.3 0.2 - - - -
122A ARG* 1.3 74.9 - - - +
124A MET* 1.3 63.7 + - - +
126A ARG* 3.3 5.0 + - - +
127A ALA* 3.0 24.8 + - - +
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Residues in contact with MET 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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101A LEU* 3.7 21.1 - - - -
120A ASN 3.2 11.6 + - - +
121A GLY* 3.1 11.6 + - - +
123A ALA* 1.3 79.7 - - - +
125A LEU* 1.3 56.5 + - - +
127A ALA 3.1 0.5 + - - -
128A PHE* 2.9 49.2 + - + -
132A VAL* 3.3 21.0 - - + +
222A ASN 3.2 35.2 - - - +
223A THR 3.8 4.5 - - - +
224A PHE* 3.8 24.0 - - + +
267A MET* 4.1 4.3 - - + -
268A MET* 3.7 28.7 - - + -
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Residues in contact with LEU 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 GLY 2.9 18.3 + - - +
122A ARG* 3.1 10.3 + - + +
124A MET* 1.3 76.1 - - - +
126A ARG* 1.3 61.5 + - + +
128A PHE 4.6 0.4 - - - +
129A PRO* 3.3 24.8 - - - +
130A GLY 4.5 1.8 + - - +
132A VAL* 3.7 29.4 - - + +
161A LEU* 4.4 11.4 - - + +
164A GLU* 3.5 43.3 - - + -
166A SER* 4.1 20.0 + - - +
167A PHE* 3.9 27.1 - - + -
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Residues in contact with ARG 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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94A GLU* 3.1 33.4 + - - +
95A SER* 4.6 12.3 + - - +
98A PHE* 3.2 53.5 - - + +
122A ARG* 3.0 18.4 + - - +
123A ALA* 3.6 4.4 - - - +
124A MET 3.2 0.2 - - - -
125A LEU* 1.3 79.6 - - + +
127A ALA* 1.3 60.5 + - - +
129A PRO* 3.6 16.0 - - - +
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Residues in contact with ALA 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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98A PHE* 3.8 18.4 - - + -
101A LEU* 4.0 17.3 - - + -
102A ALA* 5.0 4.7 - - - +
123A ALA 3.0 17.1 + - - +
124A MET 3.1 0.2 + - - -
126A ARG* 1.3 77.8 - - - +
128A PHE* 1.3 89.9 + - + +
129A PRO* 3.4 5.7 - - - +
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Residues in contact with PHE 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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101A LEU* 4.2 18.6 - - + -
124A MET* 2.9 44.8 + - + +
125A LEU 3.7 2.9 - - - +
127A ALA* 1.3 97.0 - - + +
129A PRO* 1.3 68.7 - - - +
130A GLY 3.2 0.7 + - - -
131A ASP* 3.0 15.2 + - + +
132A VAL* 3.4 14.2 - - + +
222A ASN* 3.3 48.5 - - + +
267A MET* 3.9 28.9 - - + -
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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
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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