Contacts of the helix formed by residues 99 - 114 (chain B) in PDB entry 1SA4
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 99 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A ALA* 6.1 1.2 - - - +
96B LEU* 2.9 25.0 + - - +
98B ALA* 1.3 83.0 + - - +
100B ARG* 1.3 64.7 + - - +
101B PRO* 3.3 5.6 - - - -
102B TRP* 3.1 43.0 + - - +
103B LEU* 3.3 8.4 + - - +
106B TRP* 5.4 0.4 - - - -
142B GLY* 4.2 0.9 - - - -
152B PRO* 5.5 0.9 - - - -
441B JAN 3.8 17.5 - - - -
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Residues in contact with ARG 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A GLN* 3.1 22.4 - - - +
82A ASP* 2.8 35.1 + - - +
87A VAL 3.1 24.4 + - - -
88A VAL* 3.1 22.7 + - + +
89A GLN* 3.8 7.1 - - - +
90A ILE* 4.3 10.5 - - + +
92A TYR* 3.8 3.1 + - - -
96B LEU 3.8 12.8 - - - +
97B ASP* 4.0 21.1 - - - +
99B SER* 1.3 74.5 - - - +
101B PRO* 1.3 71.1 - - + +
103B LEU* 3.0 22.5 + - + +
104B CYS* 3.1 14.7 + - - -
129B PHE* 3.3 37.3 - - + -
142B GLY 3.0 12.0 + - - +
143B GLY* 4.8 1.8 - - - -
144B PRO* 3.8 4.4 - - - +
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Residues in contact with PRO 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B SER 3.6 2.9 - - - -
100B ARG* 1.3 91.9 - - + +
102B TRP* 1.3 60.9 + - - +
104B CYS* 3.2 4.9 + - + +
105B TYR* 3.0 19.6 + - - +
130B LEU* 4.1 22.2 - - + -
133B CYS* 4.1 16.4 - - + -
140B PHE* 5.2 0.4 - - + -
141B GLY 3.3 19.3 - - - +
142B GLY* 3.3 19.3 - - - +
152B PRO* 3.6 27.8 - - + +
155B ALA* 3.6 10.0 - - + +
156B ALA* 4.2 6.7 - - + +
159B ALA* 5.1 0.3 - - - +
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Residues in contact with TRP 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B SER* 3.1 36.3 + - - +
100B ARG 3.1 0.2 - - - -
101B PRO* 1.3 80.2 - - - +
103B LEU* 1.3 56.0 + - - +
105B TYR* 3.2 9.9 + + - +
106B TRP* 2.8 81.1 + + + -
151B ALA* 3.5 41.4 - - + +
152B PRO* 4.7 9.0 - - + -
154B TYR* 3.5 34.5 - + - -
155B ALA* 3.7 11.4 - - + +
206B CYS* 5.6 0.2 - - - -
303B TRP* 5.7 0.2 - + - -
365B TYR* 3.9 12.3 - - - -
440B FPP 4.0 25.4 - - + -
441B JAN 3.7 23.6 - + + -
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Residues in contact with LEU 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A VAL* 3.7 19.7 - - + +
90A ILE* 5.3 2.7 - - + -
89B LEU* 3.6 26.0 - - + -
93B TYR* 4.2 4.3 - - + -
96B LEU* 4.1 32.3 - - + -
99B SER 3.3 6.5 + - - +
100B ARG* 3.0 27.0 + - + +
102B TRP* 1.3 79.8 - - - +
104B CYS* 1.3 62.8 + - - +
106B TRP* 4.0 17.9 - - + -
107B ILE* 3.0 32.5 + - + +
360B PHE* 3.9 29.6 - - + -
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Residues in contact with CYS 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A VAL* 4.3 4.5 - - - -
88A VAL* 3.9 17.7 - - - -
86B LEU* 4.7 6.7 - - - -
100B ARG 3.1 15.9 + - - -
101B PRO* 3.2 9.2 + - + +
103B LEU* 1.3 76.3 - - - +
105B TYR* 1.3 57.1 + - - +
107B ILE* 4.1 0.5 - - - +
108B LEU* 2.9 37.6 + - + +
126B VAL* 4.3 20.4 - - + -
129B PHE* 3.9 28.0 - - - -
130B LEU* 4.2 8.3 - - + -
159B ALA* 4.4 11.7 - - + -
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Residues in contact with TYR 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B PRO 3.0 10.2 + - - +
102B TRP* 3.7 20.4 - + - +
104B CYS* 1.3 74.0 - - - +
106B TRP* 1.3 77.1 + + - +
108B LEU* 4.7 0.4 - - - -
109B HIS* 2.8 51.0 + + + +
154B TYR* 4.3 5.0 + + - -
155B ALA* 3.6 22.9 - - + +
158B ASN* 3.5 38.8 + - + -
159B ALA* 4.1 8.9 - - - +
162B ILE* 3.9 8.1 - - + -
364B CYS* 4.2 3.1 - - - -
365B TYR* 3.6 20.5 + - - -
402B ASN* 2.7 49.1 + - - +
403B ILE* 4.0 4.0 - - + -
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Residues in contact with TRP 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B LEU* 5.3 0.4 - - - -
96B LEU* 4.7 4.5 - - + -
99B SER* 5.1 0.9 - - - -
102B TRP* 2.8 63.5 + + + +
103B LEU* 4.0 25.1 - - + +
105B TYR* 1.3 87.1 - + - +
107B ILE* 1.3 58.5 + - - +
109B HIS 4.1 0.2 - - - -
110B SER* 2.7 33.7 + - - -
360B PHE* 3.5 20.2 - - + +
361B TYR* 3.6 22.4 - + + -
364B CYS* 3.7 23.2 - - + +
365B TYR* 3.4 19.3 + + - -
441B JAN 3.5 63.9 - + + -
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Residues in contact with ILE 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A VAL* 4.4 4.9 - - + -
82B LEU* 3.6 28.0 - - + +
85B GLY 3.5 31.6 - - - +
86B LEU* 3.6 22.7 - - + +
103B LEU* 3.0 25.0 + - + +
104B CYS 4.1 1.1 - - - +
106B TRP* 1.3 74.1 - - - +
108B LEU* 1.3 65.3 + - - +
110B SER* 3.3 3.3 + - - -
111B LEU* 3.0 34.7 + - + +
360B PHE* 3.7 40.2 - - + -
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Residues in contact with LEU 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B LEU* 4.2 24.9 - - + -
104B CYS* 2.9 25.5 + - + +
105B TYR* 4.0 1.6 - - - +
107B ILE* 1.3 76.0 - - - +
109B HIS* 1.3 58.6 + - - +
111B LEU* 3.4 5.6 + - + +
112B GLU* 2.9 29.6 + - - +
118B ILE* 3.9 36.1 - - + +
126B VAL* 4.1 23.3 - - + -
159B ALA* 4.1 30.1 - - + +
162B ILE* 4.1 18.2 - - + +
163B ILE* 4.1 11.4 - - + -
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Residues in contact with HIS 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B TYR* 2.8 24.9 + - + +
106B TRP 4.1 2.5 - - - +
108B LEU* 1.3 74.6 - - - +
110B SER* 1.3 61.5 + - - +
112B GLU* 2.7 27.7 + - - +
113B LEU* 2.8 54.0 + - + +
162B ILE* 3.7 12.9 - - + +
364B CYS* 3.8 16.2 - - - -
368B SER* 3.1 20.6 + - - -
397B THR* 3.2 16.3 + - - -
402B ASN* 2.9 45.1 + - - -
403B ILE* 3.6 3.9 - - - -
404B GLY 4.4 0.2 - - - -
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Residues in contact with SER 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B LEU* 3.6 29.0 - - - +
106B TRP 2.7 22.0 + - - -
107B ILE 3.6 0.7 - - - -
109B HIS* 1.3 76.7 - - - +
111B LEU* 1.3 62.8 + - - +
113B LEU* 3.2 7.3 + - - +
114B LEU* 3.0 28.2 + - - +
360B PHE 4.8 0.2 + - - -
363B THR* 3.8 4.5 - - - +
364B CYS* 3.3 25.1 + - - -
367B LEU* 3.9 14.1 - - - +
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Residues in contact with LEU 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B PHE* 3.7 33.4 - - + +
82B LEU* 3.9 25.6 - - + -
83B LYS* 4.8 3.6 - - - +
86B LEU* 4.3 13.9 - - + -
107B ILE* 3.0 36.7 + - + +
108B LEU* 3.6 5.4 - - - +
110B SER* 1.3 75.6 - - - +
112B GLU* 1.3 62.2 + - - +
114B LEU* 3.2 3.5 + - - -
115B ASP 3.0 4.5 + - - -
116B GLU* 2.9 38.7 + - + +
117B PRO 6.0 0.2 - - - +
118B ILE* 3.7 28.7 - - + -
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Residues in contact with GLU 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B LEU 2.9 16.4 + - - +
109B HIS* 2.7 30.7 + - + +
111B LEU* 1.3 77.3 - - - +
113B LEU* 1.3 64.1 + - + +
115B ASP* 3.0 12.5 + - - +
116B GLU 5.0 2.9 - - - +
118B ILE* 5.3 2.6 - - + +
162B ILE* 3.7 25.8 - - + +
395B GLN* 3.5 16.9 - - + +
396B PRO 5.8 0.7 - - - +
404B GLY* 2.9 31.3 + - - -
406B ASP* 4.4 0.9 - - - +
407B LYS* 3.2 27.1 - - - +
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Residues in contact with LEU 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B ARG* 5.0 0.2 + - - -
109B HIS* 2.8 44.3 + - + +
110B SER* 3.2 6.7 + - - +
112B GLU* 1.3 77.6 - - + +
114B LEU* 1.3 57.1 + - - +
115B ASP* 3.1 4.0 + - - +
364B CYS 4.2 2.0 - - - +
367B LEU* 3.7 14.8 - - + -
368B SER* 3.5 40.4 - - - +
371B SER* 4.1 8.5 - - - -
394B LEU* 3.5 18.6 - - + +
395B GLN* 3.0 48.9 + - + +
396B PRO 4.4 2.9 - - - +
397B THR* 4.0 14.4 - - - -
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Residues in contact with LEU 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B LEU* 4.0 13.5 - - + -
75B ARG* 3.1 42.2 + - + +
78B HIS* 4.0 17.7 - - + -
79B PHE* 4.4 8.5 - - - +
82B LEU* 3.7 25.6 - - + -
110B SER 3.0 19.8 + - - +
111B LEU* 3.7 4.9 - - - +
112B GLU 3.2 0.2 - - - -
113B LEU* 1.3 74.7 - - - +
115B ASP* 1.3 71.0 + - - +
116B GLU* 3.2 17.8 + - + +
367B LEU* 4.3 15.0 - - + -
394B LEU* 3.7 20.6 - - + -
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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
------------------------------------------------------------
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