Contacts of the helix formed by residues 85 - 103 (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 THR 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A TYR* 5.7 1.8 - - - -
83A ALA* 3.3 4.1 - - - +
84A SER* 1.3 92.3 + - - +
86A LEU* 1.3 59.2 + - - +
87A GLU* 4.0 15.3 - - - +
88A GLU* 3.2 24.3 + - - +
89A ALA* 2.8 28.6 + - - +
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Residues in contact with LEU 86 (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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29A PHE* 4.6 3.1 - - + -
31A TYR* 4.1 26.2 - - + -
33A GLU* 3.6 47.1 - - + +
37A ARG* 5.2 6.1 - - - +
85A THR* 1.3 72.4 - - - +
87A GLU* 1.3 71.4 + - - +
89A ALA* 3.2 6.2 + - - +
90A HIS* 2.9 62.6 + - + +
115A ASP* 5.4 1.1 - - - +
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Residues in contact with GLU 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A THR* 3.1 10.9 - - - +
86A LEU* 1.3 91.7 + - - +
88A GLU* 1.3 66.6 + - - +
90A HIS* 3.3 12.1 + - - +
91A GLU* 3.1 30.5 + - - +
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Residues in contact with GLU 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ALA* 3.8 12.3 - - + -
84A SER* 3.4 26.8 + - - -
85A THR* 3.1 19.4 + - - +
87A GLU* 1.3 78.2 - - - +
89A ALA* 1.3 57.6 + - - +
91A GLU* 3.0 15.6 + - + +
92A LYS* 2.8 47.6 + - + +
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Residues in contact with ALA 89 (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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29A PHE* 3.6 14.8 - - + -
31A TYR* 3.8 33.2 - - + +
81A ILE* 3.6 10.4 - - + +
83A ALA* 3.3 10.0 - - + +
85A THR 2.8 13.6 + - - +
86A LEU* 3.3 11.9 - - - +
88A GLU* 1.3 75.8 - - - +
90A HIS* 1.3 57.6 + - - +
92A LYS* 3.3 0.9 + - - -
93A LEU* 2.9 30.8 + - - +
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Residues in contact with HIS 90 (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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29A PHE* 3.4 27.6 - + - -
86A LEU* 2.9 48.8 + - + +
87A GLU* 3.6 12.6 + - - +
89A ALA* 1.3 72.2 - - - +
91A GLU* 1.3 58.0 + - + +
93A LEU* 3.3 1.4 + - - +
94A GLU* 3.0 26.4 + - - +
115A ASP* 4.1 30.5 + - + +
119A PRO* 3.4 33.5 - - + +
122A ARG* 4.7 9.2 + - - +
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Residues in contact with GLU 91 (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 GLU* 3.1 19.7 + - - +
88A GLU* 3.0 17.8 + - + +
90A HIS* 1.3 77.7 - - + +
92A LYS* 1.3 57.7 + - + +
94A GLU* 3.4 9.3 + - - +
95A SER* 3.0 29.7 + - - -
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Residues in contact with LYS 92 (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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81A ILE* 3.6 21.8 - - + +
82A THR* 3.1 33.4 + - - +
83A ALA* 4.2 10.3 - - + -
88A GLU* 2.8 34.9 + - + +
91A GLU* 1.3 69.6 - - + +
93A LEU* 1.3 61.1 + - - +
95A SER* 3.4 5.7 + - - -
96A LYS* 3.0 31.2 + - - +
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Residues in contact with LEU 93 (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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27A ILE* 3.9 17.3 - - + -
29A PHE* 3.6 31.2 - - + -
81A ILE* 3.8 23.5 - - + +
89A ALA 2.9 18.2 + - - +
90A HIS 3.6 4.0 - - - +
92A LYS* 1.3 72.8 - - - +
94A GLU* 1.3 66.2 + - - +
96A LYS* 3.3 1.8 + - + +
97A VAL* 2.9 34.6 + - + +
109A VAL* 4.0 10.1 - - + -
116A GLN* 3.8 25.8 - - + +
119A PRO* 4.2 6.1 - - + -
120A ASN* 3.5 25.1 - - - +
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Residues in contact with GLU 94 (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 3.0 16.9 + - - +
91A GLU* 3.7 9.2 - - - +
93A LEU* 1.3 77.6 - - - +
95A SER* 1.3 62.7 + - - +
97A VAL* 4.8 0.2 - - - -
98A PHE* 2.9 24.1 + - - +
119A PRO* 3.4 26.9 - - + +
122A ARG* 2.9 40.3 + - - +
123A ALA* 3.4 12.9 - - - +
126A ARG* 3.1 32.2 + - - +
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Residues in contact with SER 95 (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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91A GLU 3.0 18.1 + - - -
92A LYS* 3.8 6.3 - - - -
94A GLU* 1.3 78.0 - - - +
96A LYS* 1.3 62.4 + - - +
98A PHE* 3.4 6.3 + - - +
99A THR* 3.1 34.6 + - - +
126A ARG* 4.6 9.1 + - - +
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Residues in contact with LYS 96 (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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19A GLU* 3.0 40.0 + - - -
27A ILE* 3.8 19.7 - - + -
78A ALA* 4.1 16.4 - - + +
81A ILE* 4.1 19.3 - - + -
92A LYS 3.0 18.2 + - - +
93A LEU* 3.7 3.4 - - - +
95A SER* 1.3 74.1 - - - +
97A VAL* 1.3 65.4 + - - +
99A THR* 2.8 27.8 + - - +
100A VAL* 3.2 12.1 + - - +
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Residues in contact with VAL 97 (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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27A ILE* 4.0 12.6 - - + -
93A LEU* 2.9 26.0 + - + +
94A GLU* 4.8 0.2 - - - -
96A LYS* 1.3 74.1 - - - +
98A PHE* 1.3 63.4 + - - +
100A VAL* 3.3 3.8 + - - +
101A LEU* 3.0 27.8 + - + +
107A PRO* 3.9 9.6 - - + -
109A VAL* 3.8 17.7 - - + -
120A ASN* 3.3 22.4 - - - +
123A ALA* 3.7 18.2 - - + -
268A MET* 3.6 31.2 - - + -
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Residues in contact with PHE 98 (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 2.9 18.5 + - - +
95A SER 3.5 2.9 - - - +
97A VAL* 1.3 77.7 - - - +
99A THR* 1.3 62.2 + - + +
101A LEU* 3.1 6.6 + - - +
102A ALA* 2.7 52.2 + - + +
123A ALA* 3.6 17.2 - - + +
126A ARG* 3.2 53.6 - - + +
127A ALA* 3.8 26.5 - - + -
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Residues in contact with THR 99 (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 SER* 3.1 21.4 + - - +
96A LYS* 2.8 29.3 + - - +
98A PHE* 1.3 87.5 - - + +
100A VAL* 1.3 65.6 + - - +
102A ALA* 3.4 5.0 + - - +
103A ARG* 3.4 32.4 + - - +
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Residues in contact with VAL 100 (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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19A GLU* 3.5 24.0 - - - +
25A VAL* 4.2 18.2 - - + -
27A ILE* 4.4 10.5 - - + -
96A LYS* 3.2 16.2 + - - +
97A VAL 3.6 6.5 - - - +
99A THR* 1.3 81.7 + - - +
101A LEU* 1.3 62.2 + - - +
103A ARG* 3.5 14.7 + - - +
105A ALA* 3.1 40.4 + - + +
106A PHE 3.9 1.8 - - - -
107A PRO* 3.6 32.3 - - + -
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Residues in contact with LEU 101 (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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97A VAL* 3.0 32.9 + - + +
98A PHE* 3.5 5.8 - - - +
100A VAL* 1.3 76.5 - - - +
102A ALA* 1.3 58.8 + - - +
104A GLY* 2.9 22.0 + - - -
105A ALA 3.9 5.6 - - - +
107A PRO* 3.6 15.5 - - + -
123A ALA* 3.9 23.6 - - + +
124A MET* 3.7 30.7 - - - -
127A ALA* 4.0 14.4 - - + -
128A PHE* 4.2 18.3 - - + -
267A MET* 3.4 27.1 - - + +
268A MET* 4.2 0.4 - - + -
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Residues in contact with ALA 102 (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* 2.7 45.1 + - + +
99A THR* 3.8 7.4 - - - +
100A VAL 3.3 0.2 - - - -
101A LEU* 1.3 74.8 - - - +
103A ARG* 1.3 56.3 + - - +
104A GLY 3.3 1.2 + - - -
127A ALA* 5.3 4.3 - - - -
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Residues in contact with ARG 103 (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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19A GLU* 2.8 47.5 + - - +
20A GLU* 4.0 40.5 + - - +
25A VAL* 3.7 14.3 - - - +
99A THR* 3.4 23.3 + - - +
100A VAL* 3.5 21.0 - - - +
101A LEU 3.2 0.2 - - - -
102A ALA* 1.3 77.5 - - - +
104A GLY* 1.3 59.1 + - - +
105A ALA* 3.5 12.6 + - + +
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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