Contacts of the helix formed by residues 90 - 107 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86D ILE* 3.7 11.5 - - + +
87D ASP* 2.7 40.3 + - - +
89D GLU* 1.3 90.7 + - - +
91D TYR* 1.3 58.0 + - - -
92D GLN 3.3 3.1 - - - -
93D SER* 3.2 15.1 + - - -
94D THR* 2.6 34.2 + - - +
132D LEU* 5.2 8.3 - - + -
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Residues in contact with TYR 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D TYR* 3.7 51.8 - + + -
52D LEU* 3.7 21.6 - - + +
81D PHE* 3.7 26.9 - + - -
86D ILE* 3.6 23.8 + - + -
87D ASP 3.2 17.9 - - - -
88D ARG* 3.2 37.4 + - + +
89D GLU 3.6 0.2 - - - -
90D ASN* 1.3 75.2 - - - +
92D GLN* 1.3 64.3 + - - +
94D THR* 3.1 13.8 + - - -
95D ALA 3.2 9.0 + - - -
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Residues in contact with GLN 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D VAL* 5.3 5.7 - - - +
52D LEU* 3.9 17.8 - - + +
55D TRP* 3.4 54.2 - - - +
88D ARG 4.8 1.0 + - - -
89D GLU 5.0 4.0 + - - +
90D ASN 3.3 0.4 - - - -
91D TYR* 1.3 78.3 - - - +
93D SER* 1.3 63.4 + - - +
95D ALA* 3.2 10.5 + - - +
96D ALA 3.3 5.5 + - - -
120D CYS* 3.5 27.5 - - + +
124D THR* 5.8 1.6 - - - +
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Residues in contact with SER 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89D GLU 4.6 4.0 + - - -
90D ASN* 3.2 17.1 + - - -
92D GLN* 1.3 79.5 - - - +
94D THR* 1.3 57.7 + - - +
96D ALA* 3.1 19.8 + - - +
97D VAL* 3.1 17.2 + - - +
120D CYS* 4.7 3.4 - - - -
124D THR* 4.0 17.0 + - - +
128D LYS* 5.9 1.8 - - - +
129D LEU* 3.7 17.5 - - - +
132D LEU* 3.6 21.1 - - - -
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Residues in contact with THR 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D LEU* 3.5 9.0 - - + +
80D LEU* 4.5 21.0 - - + +
81D PHE* 4.0 14.8 - - + -
86D ILE* 3.6 31.0 - - + +
90D ASN* 2.6 22.4 + - - +
91D TYR 3.1 8.7 + - - -
93D SER* 1.3 74.4 - - - +
95D ALA* 1.3 63.4 + - - +
97D VAL* 3.9 5.1 - - + +
98D ALA* 3.3 16.6 + - - +
132D LEU* 4.3 17.4 - - + +
136D SER* 5.4 4.7 - - - +
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Residues in contact with ALA 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D LEU* 3.8 26.5 - - + -
55D TRP* 4.0 19.1 - - + -
56D MET* 3.2 21.5 - - + +
77D LEU* 3.5 17.5 - - + +
91D TYR 3.2 3.6 + - - -
92D GLN 3.2 10.4 + - - +
93D SER 3.2 0.6 - - - -
94D THR* 1.3 78.2 - - - +
96D ALA* 1.3 61.4 + - - +
98D ALA 3.5 0.3 + - - -
99D LEU* 3.2 19.8 + - - +
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Residues in contact with ALA 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D TRP* 3.9 12.3 - - + -
92D GLN 3.3 2.2 + - - -
93D SER 3.1 11.1 + - - +
95D ALA* 1.3 76.5 - - - +
97D VAL* 1.3 53.8 + - - +
99D LEU* 3.4 4.5 + - - +
100D HIS* 2.7 36.2 + - - +
116D LEU* 3.6 10.4 - - + +
120D CYS* 3.8 27.4 - - - -
129D LEU* 4.0 21.5 - - + -
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Residues in contact with VAL 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D LEU* 5.3 2.9 - - + -
93D SER 3.1 15.2 + - - +
94D THR* 4.0 8.3 - - + +
96D ALA* 1.3 72.5 - - - +
98D ALA* 1.3 56.3 + - - +
100D HIS* 3.6 7.5 - - - +
101D ILE* 2.7 55.1 + - + +
129D LEU* 3.4 31.9 - - + +
132D LEU* 3.5 20.4 - - + -
133D GLU* 3.6 24.5 - - + -
136D SER* 3.8 14.1 - - - +
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Residues in contact with ALA 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D MET* 3.7 11.2 - - + -
73D ALA* 3.3 28.6 - - - +
76D LEU* 4.6 9.5 - - + +
77D LEU* 4.1 14.6 - - + +
80D LEU* 5.2 4.0 - - + +
94D THR 3.3 15.5 + - - +
96D ALA 3.3 0.4 - - - -
97D VAL* 1.3 77.7 - - - +
99D LEU* 1.3 59.3 + - - +
101D ILE* 3.2 6.9 + - - +
102D ALA* 2.8 31.5 + - - +
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Residues in contact with LEU 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D TRP* 3.9 16.4 - - + -
56D MET* 3.5 31.7 - - + +
59D VAL* 3.8 35.9 - - + -
60D CYS* 3.7 22.4 - - - -
69D VAL* 4.1 4.4 - - + +
70D PHE* 4.9 0.9 - - - -
73D ALA* 3.5 24.5 - - + -
95D ALA 3.2 5.3 + - - +
96D ALA* 3.5 7.9 - - - +
98D ALA* 1.3 79.2 - - - +
100D HIS* 1.3 57.6 + - - +
102D ALA* 3.1 3.0 + - - +
103D GLY* 2.8 27.9 + - - -
111D ILE* 4.0 11.8 - - + +
116D LEU* 4.3 9.4 - - + -
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Residues in contact with HIS 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C GLU* 3.1 30.1 + - - +
96D ALA 2.7 22.4 + - - +
97D VAL* 3.6 8.5 - - - +
99D LEU* 1.3 72.8 - - - +
101D ILE* 1.3 60.8 + - - +
103D GLY* 3.3 3.5 + - - -
104D LYS* 3.2 40.5 + - + +
111D ILE* 3.2 27.2 + - - +
113D ALA* 4.0 12.4 + - + -
116D LEU* 3.8 14.7 - - + +
129D LEU* 5.7 5.7 + - + +
130D LEU* 3.9 13.6 - - + +
133D GLU* 2.5 36.5 + - - +
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Residues in contact with ILE 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C ILE* 5.6 2.2 - - + -
76D LEU* 3.9 12.8 - - + -
80D LEU* 5.5 2.5 - - + -
97D VAL* 2.7 44.5 + - + +
98D ALA* 3.7 5.2 - - - +
100D HIS* 1.3 69.6 - - - +
102D ALA* 1.3 66.1 + - - +
104D LYS* 3.0 23.4 + - + +
105D VAL* 3.3 8.2 + - + +
133D GLU* 3.6 25.4 - - + +
136D SER* 4.4 7.9 - - - -
137D LEU* 3.9 29.4 - - + -
140D LEU* 4.5 8.3 - - + -
144D ALA* 3.8 28.0 - - + -
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Residues in contact with ALA 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D VAL* 3.4 31.0 - - + +
72D LEU* 3.5 21.3 - - + +
73D ALA* 3.7 13.5 - - + +
76D LEU* 5.2 0.4 - - + -
98D ALA 2.8 17.7 + - - +
99D LEU 3.5 3.8 - - - +
101D ILE* 1.3 73.5 - - - +
103D GLY* 1.3 62.2 + - - +
105D VAL* 3.0 2.1 + - - +
106D ARG* 2.8 32.7 + - - +
107D ALA 3.9 0.3 + - - -
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Residues in contact with GLY 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C ARG* 3.5 4.5 + - - -
69D VAL* 4.0 3.3 - - - +
99D LEU 2.8 14.3 + - - -
100D HIS 3.3 5.4 + - - -
101D ILE 3.2 0.4 - - - -
102D ALA* 1.3 78.0 - - - +
104D LYS* 1.3 59.8 + - - +
107D ALA* 3.0 39.0 + - - +
110D PRO* 4.2 11.3 - - - +
111D ILE* 3.8 14.8 - - - -
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Residues in contact with LYS 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C GLU* 2.6 36.3 + - - -
44C VAL* 2.9 27.9 + - + +
46C SER* 3.5 30.6 - - - +
49C ILE* 4.7 13.9 - - + -
50C ARG* 2.6 32.9 + - - +
100D HIS* 3.2 19.3 + - + +
101D ILE* 3.0 16.2 + - + +
103D GLY* 1.3 77.6 - - - +
105D VAL* 1.3 53.1 + - + +
110D PRO* 5.3 6.1 - - + -
133D GLU* 2.7 38.5 + - - +
137D LEU* 6.1 1.3 - - + -
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Residues in contact with VAL 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C ILE* 3.8 26.0 - - + -
50C ARG* 3.1 27.2 + - + +
53C SER* 5.8 2.0 - - - +
154C VAL* 3.6 10.2 - - - +
72D LEU* 3.6 16.4 - - + -
101D ILE 3.3 13.4 + - - +
102D ALA 3.0 1.8 + - - -
104D LYS* 1.3 79.6 - - - +
106D ARG* 1.3 65.9 + - - +
144D ALA* 3.9 17.7 - - + -
145D ASP* 3.5 37.0 - - + +
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Residues in contact with ARG 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C ARG* 3.7 1.7 + - - -
152C PHE* 6.2 3.8 - - - +
154C VAL* 4.3 27.6 - - + +
66D ASP* 3.6 13.6 - - + +
68D ASN* 3.5 53.3 - - + +
69D VAL* 4.0 12.6 - - + -
72D LEU* 4.0 14.7 - - + +
102D ALA 2.8 13.3 + - - +
105D VAL* 1.3 81.0 - - - +
107D ALA* 1.3 63.6 - - - +
145D ASP* 2.7 37.5 + - - -
146D ARG 2.8 20.2 + - - -
148D LEU* 3.7 11.6 - - - +
151D ASP* 3.2 24.8 + - - -
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Residues in contact with ALA 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C ARG* 2.7 28.4 + - - -
154C VAL* 5.2 0.3 - - - +
65D GLN* 3.4 24.2 - - - +
66D ASP* 3.0 7.9 - - - +
69D VAL* 3.6 8.7 - - + +
103D GLY* 3.0 30.3 + - - +
106D ARG* 1.3 79.2 - - - +
108D TYR* 1.3 62.7 + - - +
109D MET 3.9 6.5 - - - +
110D PRO* 4.1 4.4 - - + +
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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