Contacts of the helix formed by residues 90 - 107 (chain B) in PDB entry 1F5Q
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 90 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ILE* 4.1 8.0 - - + +
87B ASP* 2.8 35.8 + - - +
89B GLU* 1.3 89.6 + - - +
91B TYR* 1.3 56.8 + - - +
92B GLN 3.5 1.3 - - - -
93B SER* 3.4 15.0 + - - -
94B THR* 2.9 32.8 + - - +
132B LEU* 5.2 7.6 - - + -
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Residues in contact with TYR 91 (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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48B TYR* 3.6 54.5 + + + -
52B LEU* 4.2 17.5 - - + +
81B PHE* 3.7 21.1 - + - -
86B ILE* 3.5 31.6 + - + -
87B ASP 3.2 18.4 - - - -
88B ARG* 3.3 37.5 + - + +
89B GLU 3.4 0.4 - - - -
90B ASN* 1.3 72.6 - - - +
92B GLN* 1.3 67.8 + - - +
94B THR* 2.9 15.5 + - - -
95B ALA* 3.0 12.1 + - - +
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Residues in contact with GLN 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B VAL* 5.3 4.9 - - - +
52B LEU* 4.4 15.7 - - + +
55B TRP* 3.1 64.4 - - - +
88B ARG 4.9 0.2 + - - -
89B GLU 4.7 5.0 + - - +
90B ASN 3.5 0.2 - - - -
91B TYR* 1.3 77.8 - - - +
93B SER* 1.3 62.1 + - - +
95B ALA* 3.2 5.9 + - - +
96B ALA* 3.1 18.7 + - - +
120B CYS* 3.8 24.5 - - + +
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Residues in contact with SER 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B GLU 4.9 3.0 + - - -
90B ASN* 3.4 20.8 + - - +
91B TYR 3.1 0.4 - - - -
92B GLN* 1.3 77.0 - - - +
94B THR* 1.3 64.0 + - - +
96B ALA* 3.1 7.0 + - - +
97B VAL* 3.0 24.8 + - - +
120B CYS* 4.7 2.8 - - - -
124B THR* 4.2 15.9 + - - +
128B LYS* 6.1 0.9 - - - +
129B LEU* 3.7 21.8 - - - +
132B LEU* 4.0 12.3 - - - -
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Residues in contact with THR 94 (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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77B LEU* 3.4 19.5 - - + -
80B LEU* 4.4 18.6 - - + -
81B PHE* 3.6 16.2 - - + -
86B ILE* 3.8 24.7 - - + +
90B ASN* 2.9 19.1 + - - +
91B TYR* 2.9 10.4 + - - -
93B SER* 1.3 72.3 - - - +
95B ALA* 1.3 60.9 + - - +
97B VAL* 3.1 3.8 + - - +
98B ALA* 2.9 28.4 + - - +
132B LEU* 4.0 17.1 - - - +
136B SER* 5.7 1.6 - - - +
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Residues in contact with ALA 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B LEU* 3.9 22.9 - - + -
55B TRP* 3.9 19.9 - - + -
56B MET* 3.1 34.8 - - + +
77B LEU* 3.5 14.1 - - + +
91B TYR 3.0 10.6 + - - +
92B GLN* 3.2 11.6 + - - +
94B THR* 1.3 76.8 - - - +
96B ALA* 1.3 61.2 + - - +
99B LEU* 3.2 6.6 + - - +
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Residues in contact with ALA 96 (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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55B TRP* 4.1 11.7 - - + -
92B GLN 3.1 11.7 + - - +
93B SER 3.4 9.0 - - - +
94B THR 3.1 0.2 - - - -
95B ALA* 1.3 75.9 - - - +
97B VAL* 1.3 54.7 + - - +
99B LEU* 3.2 6.7 - - - +
100B HIS* 2.8 34.6 + - - +
116B LEU* 3.6 11.5 - - + +
120B CYS* 3.8 22.2 - - - -
129B LEU* 4.1 19.1 - - + -
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Residues in contact with VAL 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B LEU* 5.1 2.0 - - + -
93B SER 3.0 18.5 + - - +
94B THR* 3.5 9.0 - - + +
96B ALA* 1.3 73.9 - - - +
98B ALA* 1.3 56.2 + - - +
100B HIS* 3.0 6.4 + - - +
101B ILE* 2.7 57.4 + - + +
129B LEU* 3.5 31.2 - - + +
132B LEU* 3.6 19.7 - - + -
133B GLU* 3.7 13.0 - - + -
136B SER* 3.7 18.8 - - - +
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Residues in contact with ALA 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B MET* 3.8 10.1 - - + -
73B ALA* 3.4 28.0 - - - +
76B LEU* 4.4 10.5 - - + +
77B LEU* 3.9 19.3 - - + +
80B LEU* 4.9 5.6 - - + +
94B THR 2.9 15.7 + - - +
95B ALA 3.8 0.2 - - - +
97B VAL* 1.3 78.1 - - - +
99B LEU* 1.3 58.8 + - - +
101B ILE* 4.0 5.9 - - - +
102B ALA* 3.1 29.3 + - - +
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Residues in contact with LEU 99 (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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55B TRP* 3.7 31.2 - - + -
56B MET* 3.4 34.0 - - + +
59B VAL* 4.0 20.6 - - + -
60B CYS* 3.8 26.5 - - - -
69B VAL* 4.3 4.3 - - + +
70B PHE* 5.0 0.4 - - - -
73B ALA* 3.6 11.7 - - + -
95B ALA 3.2 5.8 + - - +
96B ALA 3.2 9.0 - - - +
98B ALA* 1.3 79.6 - - - +
100B HIS* 1.3 65.2 + - - +
102B ALA* 3.4 2.3 + - - +
103B GLY 3.2 17.5 + - - -
111B ILE* 3.8 16.0 - - + +
116B LEU* 4.1 10.8 - - + -
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Residues in contact with HIS 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A GLU* 2.7 50.4 + - - +
96B ALA 2.8 19.1 + - - +
97B VAL* 3.0 8.9 + - - +
99B LEU* 1.3 74.2 - - - +
101B ILE* 1.3 60.3 + - - +
103B GLY* 3.5 2.1 + - - -
104B LYS* 3.4 32.6 + - + +
111B ILE* 2.8 30.8 + - - +
113B ALA* 3.8 10.9 + - + +
116B LEU* 3.8 13.6 - - + +
129B LEU* 5.9 3.0 + - + +
130B LEU* 3.8 12.4 - - + +
133B GLU* 2.4 30.0 + - - +
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Residues in contact with ILE 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ILE* 5.5 2.2 - - + -
76B LEU* 4.0 11.2 - - + -
80B LEU* 5.5 1.3 - - + -
97B VAL* 2.7 40.5 + - + +
98B ALA* 4.0 5.6 - - - +
100B HIS* 1.3 70.1 - - - +
102B ALA* 1.3 64.3 + - - +
104B LYS* 3.3 18.9 + - + +
105B VAL* 3.5 12.0 + - + +
133B GLU* 3.6 24.5 - - + +
136B SER* 4.2 10.3 - - - -
137B LEU* 3.8 31.4 - - + +
140B LEU* 4.7 7.4 - - + -
144B ALA* 3.6 28.0 - - + -
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Residues in contact with ALA 102 (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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69B VAL* 3.4 30.1 - - + +
72B LEU* 3.7 18.0 - - + +
73B ALA* 3.6 14.4 - - + +
76B LEU* 4.5 1.5 - - + +
98B ALA 3.1 19.3 + - - +
99B LEU 3.7 4.3 - - - +
100B HIS 3.4 0.2 - - - -
101B ILE* 1.3 77.3 - - - +
103B GLY* 1.3 58.0 + - - +
105B VAL* 3.1 3.6 + - - +
106B ARG* 2.9 30.3 + - - +
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Residues in contact with GLY 103 (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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50A ARG* 3.6 4.2 + - - -
69B VAL* 4.1 1.8 - - - +
99B LEU 3.2 10.1 + - - -
100B HIS 3.5 2.2 + - - -
101B ILE 3.2 0.4 - - - -
102B ALA* 1.3 72.5 - - - +
104B LYS* 1.3 58.0 + - - +
105B VAL 2.9 7.4 + - - -
107B ALA* 2.8 37.2 + - - +
110B PRO* 5.8 1.5 - - - +
111B ILE* 3.4 33.1 - - - +
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Residues in contact with LYS 104 (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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42A GLU* 2.8 31.0 + - - -
44A VAL* 2.4 36.3 + - - +
46A SER* 3.5 32.4 - - - +
49A ILE* 4.4 16.6 - - + +
50A ARG* 2.9 24.7 + - - +
100B HIS* 3.4 30.7 + - + +
101B ILE* 3.3 13.1 + - + +
103B GLY* 1.3 74.3 - - - +
105B VAL* 1.3 59.0 + - - +
133B GLU* 2.9 23.8 + - - +
137B LEU* 5.9 1.6 - - + -
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Residues in contact with VAL 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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49A ILE* 3.8 24.0 - - + +
50A ARG* 3.3 25.6 + - + +
53A SER* 5.5 1.1 - - - +
154A VAL* 3.7 9.9 - - - +
72B LEU* 3.7 10.8 - - + -
101B ILE 3.5 14.4 - - - +
102B ALA 3.1 6.6 + - - +
103B GLY 2.9 0.6 - - - -
104B LYS* 1.3 80.6 - - - +
106B ARG* 1.3 68.4 + - - +
144B ALA* 3.9 18.4 - - + -
145B ASP* 3.3 39.3 - - + +
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Residues in contact with ARG 106 (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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50A ARG* 4.2 1.1 - - - -
152A PHE* 6.0 7.1 - - - +
154A VAL* 4.6 25.2 - - + +
6B PHE 5.3 0.3 + - - -
66B ASP* 3.1 21.1 - - - +
68B ASN* 3.1 58.6 - - + +
69B VAL* 4.1 13.0 - - + -
72B LEU* 4.0 10.1 - - + -
102B ALA 2.9 9.0 + - - +
105B VAL* 1.3 87.5 - - + +
107B ALA* 1.3 63.4 + - - +
108B TYR 3.8 0.5 + - - -
145B ASP* 2.8 25.1 + - - -
146B ARG 2.9 21.4 + - - -
148B LEU* 3.6 12.3 - - - +
151B ASP* 2.6 30.3 + - - -
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Residues in contact with ALA 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ARG* 2.8 26.7 + - - -
154A VAL* 5.4 1.0 - - - +
65B GLN* 3.5 21.3 - - - +
66B ASP* 4.2 2.7 - - - -
69B VAL* 3.9 8.2 - - + +
103B GLY* 2.8 37.5 + - - +
106B ARG* 1.3 73.0 - - - +
108B TYR* 1.3 64.8 + - - +
109B MET 3.7 12.6 - - - +
110B PRO* 4.9 2.7 - - + +
111B ILE* 4.2 2.9 - - + -
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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
------------------------------------------------------------
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