Contacts of the helix formed by residues 85 - 104 (chain A) in PDB entry 2HXO
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 85 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A ALA 3.3 3.1 + - - -
84A ASP* 1.3 76.8 - - - +
86A PRO* 1.3 76.0 - - - +
87A GLN* 3.3 19.4 + - - +
88A ASP* 3.0 21.3 + - - -
89A ALA* 3.1 21.7 + - - +
134A GLN* 4.7 0.2 - - - -
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Residues in contact with PRO 86 (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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85A SER* 1.3 88.9 - - - +
87A GLN* 1.3 66.5 + - - +
89A ALA* 3.3 3.3 + - - +
90A VAL* 3.0 32.7 + - - +
134A GLN* 3.1 39.7 - - + +
137A ALA* 3.6 28.9 - - + +
138A MSE 3.7 9.2 - - + -
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Residues in contact with GLN 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A SER* 3.2 9.7 + - - +
86A PRO* 1.3 92.6 - - - +
88A ASP* 1.3 61.1 + - - +
90A VAL* 3.3 5.5 + - - +
91A ARG* 3.0 44.5 + - - +
138A MSE 3.6 17.4 - - + +
225A LEU* 3.7 30.9 - - + +
229A THR* 3.3 28.4 - - + +
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Residues in contact with ASP 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ALA 3.5 6.1 - - - +
84A ASP* 3.5 28.0 - - - +
85A SER* 3.0 32.7 + - - +
87A GLN* 1.3 73.6 - - - +
89A ALA* 1.3 60.8 + - - +
91A ARG* 3.0 26.2 + - - +
92A ALA* 2.9 28.5 + - - +
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Residues in contact with ALA 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ASP* 5.0 7.4 - - + -
85A SER 3.1 11.7 + - - +
86A PRO 3.5 9.0 - - - +
88A ASP* 1.3 77.3 - - - +
90A VAL* 1.3 62.5 + - - +
92A ALA* 3.1 8.7 + - - +
93A VAL* 3.0 28.1 + - + +
134A GLN* 3.5 29.4 - - + +
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Residues in contact with VAL 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A PRO 3.0 17.8 + - - +
87A GLN 3.6 7.2 - - - +
88A ASP 3.2 0.4 - - - -
89A ALA* 1.3 75.4 - - - +
91A ARG* 1.3 58.6 + - - +
93A VAL* 3.2 9.7 + - - +
94A ALA* 2.9 26.9 + - + +
131A LEU* 4.2 21.7 - - + +
134A GLN* 3.5 23.6 - - + -
135A VAL* 5.4 0.4 - - + +
138A MSE 5.2 2.0 - - - -
152A LEU* 4.1 22.2 - - + -
221A ILE* 4.3 8.5 - - + -
225A LEU* 3.8 33.4 - - + -
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Residues in contact with ARG 91 (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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87A GLN* 3.0 42.2 + - - +
88A ASP* 3.0 35.1 + - - +
90A VAL* 1.3 78.3 - - - +
92A ALA* 1.3 56.5 + - - +
94A ALA* 3.3 6.2 + - - +
95A LEU* 2.8 37.8 + - + +
218A LEU* 4.3 19.5 - - + -
221A ILE* 3.9 19.1 - - + -
222A THR* 3.0 40.4 + - - +
225A LEU* 4.3 7.9 - - + +
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Residues in contact with ALA 92 (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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75A VAL 4.8 9.6 - - - +
84A ASP* 5.8 2.9 - - - +
88A ASP 2.9 12.0 + - - +
89A ALA* 3.1 12.1 + - - +
91A ARG* 1.3 72.5 - - - +
93A VAL* 1.3 67.4 + - + +
95A LEU* 4.0 7.2 - - - +
96A GLY* 2.9 21.1 + - - -
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Residues in contact with VAL 93 (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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75A VAL* 4.1 28.3 - - + +
89A ALA* 3.0 21.4 + - + +
90A VAL* 3.5 8.5 - - - +
92A ALA* 1.3 79.1 - - + +
94A ALA* 1.3 63.6 + - - +
96A GLY* 3.3 1.2 + - - -
97A LEU* 3.1 35.3 + - + +
127A ILE* 4.7 6.5 - - + -
130A SER* 4.0 28.9 - - - +
131A LEU* 3.9 24.7 - - + -
134A GLN* 6.0 0.7 - - + -
156A ILE* 5.3 0.4 - - + -
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Residues in contact with ALA 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A VAL 2.9 16.0 + - - +
91A ARG* 3.7 4.7 - - - +
93A VAL* 1.3 75.0 - - - +
95A LEU* 1.3 59.8 - - + +
97A LEU* 3.2 5.2 + - - +
98A TRP 2.8 24.6 + - - -
156A ILE* 3.7 28.7 - - + +
217A PHE* 3.2 28.2 - - + -
218A LEU* 5.6 0.4 - - + -
221A ILE* 4.3 15.3 - - + -
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Residues in contact with LEU 95 (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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91A ARG* 2.8 27.7 + - + +
92A ALA* 4.1 5.4 - - - +
94A ALA* 1.3 68.9 - - - +
96A GLY* 1.3 62.6 + - - +
98A TRP* 4.1 4.7 - - + -
99A ASP* 2.7 38.1 + - - +
214A ARG* 4.0 41.1 - - + +
217A PHE* 3.9 13.0 - - + -
218A LEU* 3.3 43.3 - - + -
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Residues in contact with GLY 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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74A ALA* 3.5 31.5 - - - +
75A VAL* 4.4 3.8 - - - -
92A ALA 2.9 17.4 + - - -
93A VAL 3.7 2.2 - - - -
94A ALA 3.2 0.2 - - - -
95A LEU* 1.3 77.9 - - - +
97A LEU* 1.3 56.9 + - - +
99A ASP* 3.9 3.4 - - - +
100A ALA* 3.0 30.3 + - - +
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Residues in contact with LEU 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A VAL* 3.8 39.3 - - + -
75A VAL* 4.3 6.7 - - + -
93A VAL* 3.1 21.6 + - + +
94A ALA 3.5 6.7 - - - +
96A GLY* 1.3 74.4 - - - +
98A TRP* 1.3 64.0 + - - +
100A ALA* 3.3 3.7 + - + +
101A THR* 3.0 34.2 + - + +
107A LEU* 5.6 1.1 - - + -
111A LEU* 5.0 14.8 - - + -
127A ILE* 4.2 30.3 - - + -
153A MSE 5.2 4.5 - - - -
156A ILE* 3.8 30.7 - - + -
157A LEU* 5.6 2.2 - - + -
160A ALA* 5.1 1.3 - - + -
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Residues in contact with TRP 98 (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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94A ALA 2.8 20.7 + - - +
95A LEU* 3.6 6.3 - - + +
97A LEU* 1.3 72.7 - - - +
99A ASP* 1.3 82.0 + - - +
101A THR* 3.1 19.5 + - - -
102A GLU* 3.2 26.0 + - - +
159A ALA* 3.7 12.3 - - + -
160A ALA* 3.9 17.7 - - - +
163A ASN* 3.3 44.8 + - + -
213A ASP* 3.7 26.0 - - + -
214A ARG* 3.7 39.3 - - + +
217A PHE* 3.4 45.0 - + + -
154B HIS* 6.5 0.4 - + - -
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Residues in contact with ASP 99 (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 ALA* 6.1 0.7 - - + -
95A LEU* 2.7 25.8 + - - +
96A GLY* 4.1 3.7 - - - +
98A TRP* 1.3 88.4 - - - +
100A ALA* 1.3 57.5 + - - +
102A GLU* 3.2 13.9 + - - +
103A ALA* 2.9 29.3 + - - +
214A ARG* 3.1 32.4 + - - -
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Residues in contact with ALA 100 (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 VAL* 4.0 11.4 - - + +
71A VAL* 5.3 2.5 - - - -
74A ALA* 3.7 19.9 - - + +
96A GLY 3.0 19.7 + - - +
97A LEU* 3.7 5.2 - - + +
99A ASP* 1.3 73.8 - - - +
101A THR* 1.3 57.6 + - - +
102A GLU 3.0 4.9 - - - -
103A ALA* 3.1 5.1 + - - -
104A HIS* 2.8 36.4 + - - +
107A LEU* 3.6 18.4 - - + -
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Residues in contact with THR 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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97A LEU* 3.0 19.0 + - + +
98A TRP 3.1 12.0 + - - -
100A ALA* 1.3 75.5 - - - +
102A GLU* 1.3 58.2 + - - +
104A HIS 3.3 21.7 - - - +
105A PRO* 3.7 8.1 - - - +
107A LEU* 3.7 22.7 - - + -
108A ALA* 4.5 14.1 - - - +
111A LEU* 4.3 15.3 - - + -
160A ALA* 3.8 32.3 + - + +
163A ASN* 4.1 3.9 + - - -
164A ALA* 4.2 10.9 - - - +
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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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98A TRP* 3.2 28.7 + - - +
99A ASP* 3.3 17.9 - - - +
100A ALA 3.0 0.4 - - - -
101A THR* 1.3 80.0 - - - +
103A ALA* 1.3 63.0 + - - +
104A HIS 3.3 0.2 - - - -
105A PRO* 4.4 8.5 - - - +
163A ASN* 3.5 28.4 + - - +
164A ALA* 5.9 1.3 - - - +
214A ARG* 5.5 2.9 + - - -
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Residues in contact with ALA 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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29A ASP* 4.5 5.9 - - - +
99A ASP 2.9 14.6 + - - +
100A ALA* 3.8 1.8 - - - +
102A GLU* 1.3 77.9 - - - +
104A HIS* 1.3 82.2 + - + +
105A PRO* 3.6 6.4 - - - +
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Residues in contact with HIS 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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25A VAL* 3.7 15.0 - - + +
29A ASP* 2.8 33.0 + - - -
70A VAL* 3.8 22.5 - - + +
100A ALA* 2.8 17.6 + - - +
101A THR* 3.3 8.0 - - - +
103A ALA* 1.3 94.8 - - + +
105A PRO* 1.3 60.5 - - - +
106A TRP* 3.2 32.1 - + + +
107A LEU* 2.9 29.9 + - + +
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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
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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