Contacts of the helix formed by residues 88 - 107 (chain A) in PDB entry 4D0N
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 88 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A SER* 2.8 13.2 + - - +
86A ILE 3.1 1.2 - - - -
87A ASP* 1.3 88.3 + - - +
89A PRO* 1.3 64.1 - - - +
90A ASP* 3.7 8.7 + - - +
91A SER* 2.7 51.8 + - - -
92A LEU* 3.3 4.2 + - - +
131A LEU* 4.9 0.9 - - - -
139A VAL* 4.3 1.3 - - - -
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Residues in contact with PRO 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ILE 4.6 0.4 - - - +
87A ASP 3.9 5.8 - - - +
88A SER* 1.3 86.9 - - - +
90A ASP* 1.3 62.3 + - - +
92A LEU* 3.1 7.5 + - + +
93A GLU* 3.1 27.1 + - + +
131A LEU* 3.9 12.8 - - + -
136A GLN* 3.9 24.7 - - + +
137A GLU 3.0 28.0 - - - +
138A PRO 4.8 0.2 - - - -
139A VAL* 4.0 19.1 - - + -
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Residues in contact with ASP 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ASP* 4.7 0.2 - - - -
88A SER* 3.1 8.0 + - - +
89A PRO* 1.3 78.3 - - - +
91A SER* 1.3 60.8 + - - +
92A LEU 3.3 0.7 + - - -
93A GLU* 3.4 8.4 + - - +
94A ASN* 3.3 27.6 + - - +
136A GLN* 3.0 30.3 + - - -
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Residues in contact with SER 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ASP* 3.6 29.3 - - - +
16A CYS* 5.0 3.6 - - - -
83A CYS 4.8 0.7 - - - +
84A PHE* 3.3 13.8 - - - +
85A SER* 2.8 30.9 + - - -
88A SER* 2.7 33.8 + - - -
90A ASP* 1.3 76.1 - - - +
92A LEU* 1.3 58.6 + - - +
94A ASN* 3.7 9.1 + - - +
95A ILE* 3.7 10.4 + - - +
99A TRP* 5.4 0.7 - - - -
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Residues in contact with LEU 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A PHE* 3.6 46.2 - - + -
88A SER 3.3 1.5 + - - +
89A PRO* 3.1 15.0 + - + +
91A SER* 1.3 77.6 + - - +
93A GLU* 1.3 71.3 + - - +
94A ASN 3.1 1.8 - - - -
95A ILE* 3.0 27.7 + - + +
96A PRO* 3.3 4.7 - - - +
139A VAL* 3.7 26.7 - - + -
143A GLU* 4.6 17.7 - - + +
144A GLY* 5.2 0.4 - - - -
147A MET* 3.7 32.0 - - + +
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Residues in contact with GLU 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A PRO* 3.1 13.9 + - + +
90A ASP* 3.4 8.9 + - - +
92A LEU* 1.3 86.5 - - - +
94A ASN* 1.3 60.6 + - - +
96A PRO* 3.3 9.2 - - - +
97A GLU* 3.1 47.2 - - - +
147A MET* 4.1 17.9 - - - +
150A ARG* 5.4 2.1 + - - -
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Residues in contact with ASN 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ASP* 2.6 40.7 + - - +
90A ASP* 3.3 15.5 + - - +
91A SER 3.9 4.7 - - - +
92A LEU 3.1 1.4 - - - -
93A GLU* 1.3 75.9 - - - +
95A ILE* 1.3 60.2 + - - +
96A PRO 3.5 0.2 - - - -
97A GLU* 3.8 8.5 - - - +
98A LYS* 2.8 39.4 + - + +
99A TRP* 3.1 15.0 + - + -
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Residues in contact with ILE 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A MET* 3.6 35.9 - - + -
83A CYS 3.6 29.6 - - - +
84A PHE* 4.0 9.9 - - + -
91A SER 3.7 10.3 - - - +
92A LEU* 3.0 18.6 + - + +
94A ASN* 1.3 77.9 - - - +
96A PRO* 1.3 64.8 - - + +
99A TRP* 3.4 9.3 + - + -
100A THR* 2.8 31.5 + - - -
114A LEU* 3.8 23.6 - - + -
147A MET* 4.1 9.4 - - + -
151A ILE* 3.8 13.9 - - + -
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Residues in contact with PRO 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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92A LEU 3.3 10.3 - - - +
93A GLU* 3.3 15.0 - - - +
95A ILE* 1.3 98.1 - - + +
97A GLU* 1.3 65.8 + - + +
100A THR* 3.7 10.9 - - - +
101A PRO* 3.2 21.1 - - - +
147A MET* 3.6 28.5 - - + -
150A ARG* 6.4 0.4 - - + -
151A ILE* 4.2 8.7 - - + -
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Residues in contact with GLU 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A GLU* 3.1 42.5 - - - +
94A ASN* 3.4 9.5 + - - +
95A ILE 3.3 0.8 - - - -
96A PRO* 1.3 87.2 - - + +
98A LYS* 1.3 58.0 + - + +
101A PRO* 3.8 11.1 - - - +
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Residues in contact with LYS 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ASP* 4.7 5.5 + - - +
64A GLU* 3.5 24.4 + - - +
67A ASP* 4.9 3.1 - - - -
70A ARG* 4.0 16.9 - - - +
94A ASN* 2.8 29.4 + - - +
97A GLU* 1.3 74.0 - - - +
99A TRP* 1.3 104.1 + - + +
100A THR 3.5 1.3 - - - -
101A PRO* 3.5 6.1 - - - +
102A GLU* 3.5 24.9 + - - +
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Residues in contact with TRP 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A VAL* 3.9 20.2 - - + -
12A GLY* 3.3 38.6 - - - -
13A ASP* 2.9 31.3 + - - +
60A THR* 5.6 1.6 - - - -
64A GLU* 4.7 10.1 - - + -
70A ARG* 3.6 20.4 - - - -
74A TYR* 3.9 6.1 - - - -
82A MET* 3.9 21.5 - - + -
91A SER 5.4 0.4 - - - -
94A ASN* 3.1 28.3 + - + -
95A ILE* 3.7 13.7 - - + +
98A LYS* 1.3 105.1 - - + +
100A THR* 1.3 61.3 + - - +
102A GLU* 3.4 28.5 + - - +
103A VAL* 2.9 34.9 + - + +
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Residues in contact with THR 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A MET* 3.8 17.2 - - + -
95A ILE 2.8 25.3 + - - -
96A PRO* 4.0 7.4 - - - +
99A TRP* 1.3 73.1 - - - +
101A PRO* 1.3 71.9 - - + +
103A VAL* 4.0 0.3 - - - +
104A LYS* 3.0 53.8 + - + +
112A ILE* 5.5 0.2 - - + -
151A ILE* 3.5 32.3 - - + +
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Residues in contact with PRO 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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96A PRO 3.2 19.7 - - - +
97A GLU 3.8 14.1 - - - +
98A LYS 3.5 13.7 - - - +
100A THR* 1.3 94.1 - - + +
102A GLU* 1.3 59.7 + - - +
104A LYS* 4.3 2.8 - - + +
105A HIS* 3.1 26.9 + - - +
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Residues in contact with GLU 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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70A ARG* 2.7 43.5 + - - -
71A PRO* 5.5 2.0 - - - -
74A TYR* 2.5 38.6 + - + +
98A LYS* 3.5 22.4 + - - +
99A TRP* 3.4 13.7 + - - +
100A THR 3.3 0.6 - - - -
101A PRO* 1.3 77.7 - - - +
103A VAL* 1.3 57.6 + - - +
105A HIS* 3.3 3.6 + - - +
106A PHE* 3.0 46.2 + - + -
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Residues in contact with VAL 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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11A VAL* 4.0 21.1 - - + -
74A TYR* 4.1 22.9 - - + +
80A ILE* 3.8 29.8 - - + -
82A MET* 3.9 15.0 - - + -
99A TRP* 2.9 22.1 + - + +
100A THR 4.1 0.7 - - - +
102A GLU* 1.3 76.7 - - - +
104A LYS* 1.3 55.5 + - - +
107A CYS* 2.7 46.2 + - + +
110A VAL 5.5 1.3 - - - +
112A ILE* 4.1 21.1 - - + -
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Residues in contact with LYS 104 (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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100A THR* 3.0 36.0 + - + +
101A PRO* 4.3 2.9 - - + +
103A VAL* 1.3 77.4 - - - +
105A HIS* 1.3 62.3 + - - +
107A CYS 4.2 6.1 - - - +
108A PRO* 3.3 26.2 - - + +
109A ASN 5.7 1.3 - - - +
112A ILE* 4.0 22.0 - - + -
151A ILE* 2.6 34.0 + - - +
152A GLY* 4.4 5.5 - - - +
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Residues in contact with HIS 105 (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 PRO 3.1 20.3 + - - +
102A GLU* 3.7 3.1 - - - +
104A LYS* 1.3 79.7 - - - +
106A PHE* 1.3 100.3 + + - +
108A PRO* 3.8 8.8 - - - +
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Residues in contact with PHE 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A PRO* 3.6 34.8 - - + -
74A TYR* 3.4 40.7 - + + +
75A PRO* 5.3 4.1 - - + +
102A GLU* 3.0 38.2 + - + +
105A HIS* 1.3 103.3 - + - +
107A CYS* 1.3 62.7 + - - +
108A PRO* 3.6 6.3 - - - +
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Residues in contact with CYS 107 (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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74A TYR* 3.6 47.1 - - - -
77A THR* 4.3 5.4 - - - -
80A ILE* 4.2 13.2 - - - -
103A VAL* 2.7 29.0 + - + +
104A LYS* 3.6 4.1 - - - +
106A PHE* 1.3 79.5 - - - +
108A PRO* 1.3 66.4 - - - +
109A ASN 3.3 0.9 + - - -
110A VAL* 3.2 36.7 + - + +
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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
------------------------------------------------------------
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