Contacts of the helix formed by residues 98 - 112 (chain E) in PDB entry 1S89
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 ASN 98 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B ARG* 3.8 18.4 - - - +
19E HIS* 4.4 2.5 + - - -
67E PRO* 3.9 19.9 - - + +
71E ASP* 2.7 26.1 + - - -
96E VAL* 3.2 23.2 - - - +
97E PRO* 1.3 75.8 - - - +
99E ASP* 1.3 62.3 + - - +
100E PRO* 3.3 3.4 - - - -
101E ASP* 3.1 19.6 + - - +
102E VAL* 3.0 24.1 + - - +
205E PGA 3.3 23.1 + - - +
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Residues in contact with ASP 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95E ALA* 6.4 1.1 - - + -
96E VAL* 3.3 28.2 + - + +
97E PRO 3.2 1.8 - - - +
98E ASN* 1.3 76.8 - - - +
100E PRO* 1.3 72.0 - - + +
102E VAL* 3.1 5.5 + - - +
103E LYS* 3.0 54.2 + - - +
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Residues in contact with PRO 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B PRO* 3.5 31.5 - - + +
103B LYS* 3.8 21.1 - - + +
104B ALA* 3.8 9.0 - - - +
107B ARG* 4.5 8.3 - - + -
97E PRO 3.8 7.4 - - - +
98E ASN 3.4 1.8 - - - -
99E ASP* 1.3 96.7 - - + +
101E ASP* 1.3 62.2 + - - +
103E LYS* 3.3 2.0 + - + -
104E ALA* 2.7 36.0 + - - +
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Residues in contact with ASP 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B GLN* 5.3 0.9 - - - +
104B ALA* 3.6 15.6 - - - +
107B ARG* 2.8 46.1 + - - -
108B LEU* 4.5 0.7 - - - +
66E GLY 4.6 1.2 - - - +
69E GLY* 5.3 0.5 - - - -
71E ASP* 3.5 27.8 - - + +
72E GLN* 3.1 24.0 + - + +
98E ASN* 3.1 11.0 + - - +
100E PRO* 1.3 82.7 - - - +
102E VAL* 1.3 58.8 + - - +
104E ALA* 3.6 2.8 - - - +
105E LEU* 2.9 30.3 + - - +
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Residues in contact with VAL 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E HIS* 3.5 29.6 - - + +
71E ASP* 4.4 2.0 - - - +
88E PHE* 3.7 29.6 - - + -
90E TRP* 4.3 15.5 - - + -
96E VAL* 4.3 3.1 - - + -
98E ASN* 3.0 25.0 + - - +
99E ASP* 3.1 10.1 + - - +
101E ASP* 1.3 76.2 - - - +
103E LYS* 1.3 74.5 + - + +
105E LEU* 3.4 3.3 + - - +
106E LEU* 3.1 35.2 + - + +
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Residues in contact with LYS 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B PRO* 3.8 18.7 - - + +
90D TRP* 5.4 1.6 - - - -
103D LYS* 4.4 35.7 - - + -
90E TRP* 4.1 30.5 - - - -
99E ASP* 3.0 43.9 + - - +
100E PRO* 3.7 4.5 - - + +
102E VAL* 1.3 83.6 - - + +
104E ALA* 1.3 59.8 + - - +
106E LEU* 3.4 12.0 + - + +
107E ARG* 2.9 29.5 + - - +
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Residues in contact with ALA 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B GLN* 3.2 28.3 + - + +
100B PRO* 3.9 2.7 - - - +
101B ASP* 3.8 33.5 - - - +
104B ALA* 4.6 2.7 - - + -
72E GLN* 6.0 0.2 - - + -
100E PRO 2.7 22.8 + - - +
101E ASP* 3.6 8.5 - - - +
103E LYS* 1.3 74.0 - - - +
105E LEU* 1.3 61.5 + - - +
107E ARG* 3.2 5.2 + - - +
108E LEU* 3.0 18.4 + - - +
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Residues in contact with LEU 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B GLN* 4.0 6.4 + - - +
17E VAL* 5.0 6.1 - - + -
71E ASP* 3.7 24.7 - - + +
74E VAL* 3.9 12.8 - - + -
75E GLY* 3.6 34.5 - - - +
78E ILE* 3.9 16.2 - - + -
86E LEU* 4.2 14.1 - - + -
88E PHE* 3.9 28.0 - - + -
101E ASP 2.9 17.8 + - - +
102E VAL 3.7 5.2 - - - +
103E LYS 3.3 0.2 - - - -
104E ALA* 1.3 76.3 - - - +
106E LEU* 1.3 62.6 + - - +
108E LEU* 3.3 2.5 + - - +
109E ALA* 3.0 21.5 + - - +
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Residues in contact with LEU 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D TRP* 4.7 6.7 - - + -
106D LEU* 6.4 2.7 - - + -
86E LEU* 4.7 3.8 - - + -
88E PHE* 4.2 19.1 - - + -
90E TRP* 4.3 23.6 - - + +
102E VAL* 3.1 28.1 + - + +
103E LYS* 3.9 12.6 - - + +
104E ALA 3.3 0.2 - - - -
105E LEU* 1.3 73.2 - - - +
107E ARG* 1.3 65.9 + - - +
109E ALA* 3.2 4.5 + - - +
110E THR* 2.9 28.6 + - - +
116E VAL* 4.4 15.9 - - + -
118E THR* 4.1 22.2 - - + -
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Residues in contact with ARG 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B GLY 4.1 1.8 + - - -
67B PRO* 2.8 39.2 + - - +
97B PRO 4.0 15.7 - - - -
98B ASN* 3.9 8.8 - - - +
100B PRO* 4.4 7.6 - - + -
101B ASP* 2.8 42.7 + - - -
90D TRP* 3.8 21.0 - - + -
92D PRO* 3.2 35.2 + - + +
93D LEU* 3.5 11.5 - - - +
103E LYS 2.9 18.1 + - - +
104E ALA* 3.2 4.0 + - - +
106E LEU* 1.3 76.9 - - - +
108E LEU* 1.3 68.6 + - - +
110E THR* 3.1 5.7 + - - -
111E VAL* 2.9 39.1 + - - +
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Residues in contact with LEU 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B PRO 4.2 2.2 - - - +
68B MET 3.7 30.1 - - - +
69B GLY* 3.8 14.8 - - - +
72B GLN* 3.1 35.4 - - + +
75E GLY* 3.3 29.8 - - - +
78E ILE* 4.6 4.9 - - + -
79E SER* 4.3 2.7 - - - +
104E ALA 3.0 7.6 + - - +
105E LEU* 3.7 7.4 - - - +
106E LEU 3.3 0.2 - - - -
107E ARG* 1.3 86.8 - - - +
109E ALA* 1.3 61.4 + - - +
111E VAL* 4.2 4.5 - - + -
112E TRP* 2.9 51.4 + - + +
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Residues in contact with ALA 109 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D ASN* 3.2 16.1 + - - -
78E ILE* 4.5 6.5 - - + +
86E LEU* 4.0 16.6 - - + -
105E LEU 3.0 16.8 + - - +
106E LEU* 3.2 7.2 + - - +
108E LEU* 1.3 75.6 - - - +
110E THR* 1.3 63.0 + - - +
113E ASN 3.4 9.7 + - - -
114E ILE* 3.5 20.9 + - + +
116E VAL* 3.5 25.6 - - + -
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Residues in contact with THR 110 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D TRP* 3.5 28.9 + - + +
92D PRO* 4.0 22.4 - - + -
118D THR* 3.6 34.4 + - - +
119D ASN* 3.9 14.3 + - + +
106E LEU* 2.9 15.0 + - - +
107E ARG 3.3 8.3 - - - -
109E ALA* 1.3 77.3 - - - +
111E VAL* 1.3 63.5 + - - +
113E ASN* 3.1 15.2 + - - +
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Residues in contact with VAL 111 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B PRO 4.7 1.1 - - - +
68B MET* 3.9 33.9 - - + -
92D PRO* 3.5 28.0 - - + -
93D LEU* 3.9 10.8 - - + -
107E ARG* 2.9 35.9 + - - +
108E LEU* 3.6 12.8 - - + +
110E THR* 1.3 79.1 - - - +
112E TRP* 1.3 68.4 + - + +
113E ASN* 3.2 5.9 + - - +
141E PRO* 3.6 17.7 - - + +
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Residues in contact with TRP 112 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B LEU* 4.5 5.4 - - + -
68B MET* 3.0 56.1 + - + -
6E ARG* 5.5 3.2 + - - -
78E ILE* 4.0 23.3 - - + +
79E SER* 3.6 33.8 - - - +
81E GLY* 6.0 1.6 - - - -
108E LEU* 2.9 43.3 + - + +
109E ALA 4.7 0.9 - - - +
111E VAL* 1.3 75.4 - - + +
113E ASN* 1.3 69.7 + - - +
114E ILE* 3.5 12.2 + - + +
138E ILE* 4.0 0.3 - - - +
140E ILE* 3.6 38.9 - - + +
141E PRO* 4.1 24.9 - - + -
143E TYR* 4.4 17.7 - + + -
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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