Contacts of the helix formed by residues 75 - 94 (chain A) in PDB entry 4DOH
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 LYS 75 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A ASP 4.1 4.0 + - - -
74A THR* 1.3 69.4 - - - +
76A PRO* 1.3 67.7 - - + +
77A ALA* 3.2 6.7 - - + +
78A ASN* 2.5 35.1 + - - +
79A ARG 3.3 7.3 + - - -
137A GLU* 2.9 30.8 + - - +
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Residues in contact with PRO 76 (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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30A LEU 3.5 4.2 - - - +
31A GLY* 3.3 35.9 + - - +
74A THR 3.2 4.7 - - - +
75A LYS* 1.3 87.6 - - + +
77A ALA* 1.3 66.2 + - - +
78A ASN 3.0 1.0 + - - -
79A ARG* 3.1 41.9 + - - +
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Residues in contact with ALA 77 (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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30A LEU 5.1 0.7 - - - +
31A GLY* 4.0 6.4 - - - -
32A SER 5.4 1.3 - - - +
75A LYS* 3.2 5.6 - - + +
76A PRO* 1.3 80.3 - - - +
78A ASN* 1.3 66.2 + - - +
80A CYS* 4.6 5.9 + - - +
81A CYS 4.9 0.5 + - - -
131A THR 5.4 1.7 - - - +
133A HIS* 3.7 32.2 + - + +
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Residues in contact with ASN 78 (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 THR* 3.6 14.1 - - + -
75A LYS* 2.5 22.8 + - - +
77A ALA* 1.3 79.9 - - - +
79A ARG* 1.3 61.2 + - - -
80A CYS 3.4 0.4 - - - -
81A CYS 3.3 3.3 + - - -
82A LEU* 3.2 19.1 + - - +
133A HIS* 4.0 7.2 - - - +
135A GLY* 3.3 26.5 + - - -
137A GLU* 3.0 38.8 + - - +
138A ALA* 3.6 22.8 - - + +
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Residues in contact with ARG 79 (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 ASN* 3.2 27.5 + - - +
30A LEU* 4.0 13.7 - - + -
71A LEU* 3.4 37.7 + - + +
72A GLN* 3.2 28.4 + - - +
74A THR* 2.9 25.9 + - - +
75A LYS 3.3 2.6 + - - +
76A PRO* 3.1 34.2 + - - +
78A ASN* 1.3 73.3 - - - +
80A CYS* 1.3 67.5 + - - +
82A LEU* 3.1 4.6 + - - +
83A LEU* 2.9 24.9 + - - +
175A THR* 4.5 5.8 - - - -
176A GLU* 3.1 26.9 + - - -
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Residues in contact with CYS 80 (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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30A LEU* 3.7 33.7 - - + +
33A CYS* 3.7 26.0 - - + -
76A PRO 4.2 1.0 + - - -
77A ALA 5.0 3.4 - - - +
78A ASN 3.4 0.6 - - - -
79A ARG* 1.3 79.3 - - - +
81A CYS* 1.3 63.4 + - - +
83A LEU* 3.9 1.4 - - - +
84A ARG* 3.0 20.4 + - - +
123A LEU* 4.0 11.0 - - - +
126A CYS* 4.1 1.6 - - - -
131A THR 4.1 5.2 - - - +
132A CYS* 2.0 49.2 - - - -
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Residues in contact with CYS 81 (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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77A ALA 4.9 0.2 + - - -
78A ASN 3.3 7.5 + - - +
79A ARG 3.2 0.8 - - - -
80A CYS* 1.3 82.8 - - - +
82A LEU* 1.3 64.2 + - - +
84A ARG* 3.4 3.0 + - - +
85A HIS* 3.2 36.0 + - - -
132A CYS* 3.7 8.8 - - - +
133A HIS 3.2 21.0 + - - +
134A CYS* 2.0 51.8 - - - -
138A ALA* 3.6 13.7 - - + -
139A MET* 4.3 3.8 - - - -
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Residues in contact with LEU 82 (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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69A GLU 4.0 21.1 - - - +
71A LEU* 4.2 19.3 - - + -
74A THR* 4.4 11.2 - - + +
78A ASN 3.2 10.0 + - - +
79A ARG* 3.1 10.7 + - - +
81A CYS* 1.3 81.9 - - - +
83A LEU* 1.3 61.0 + - - +
85A HIS* 3.3 5.7 + - - +
86A LEU* 3.0 42.1 + - + +
138A ALA* 4.2 15.5 - - + +
141A LYS* 4.7 10.3 - - + -
142A TYR* 4.0 31.0 - - + +
145A ILE* 4.8 3.8 - - + -
171A TRP* 5.4 0.9 - - + -
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Residues in contact with LEU 83 (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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28A LEU* 4.6 10.5 - - + -
30A LEU* 4.3 23.8 - - + -
71A LEU* 4.5 17.5 - - + +
79A ARG 2.9 16.0 + - - +
80A CYS* 3.9 4.9 - - - +
82A LEU* 1.3 75.4 - - - +
84A ARG* 1.3 61.3 + - - +
86A LEU* 3.2 10.2 + - + +
87A LEU* 2.9 41.4 + - + +
119A ILE* 5.0 5.4 - - + -
123A LEU* 4.0 17.9 - - + -
168A LEU* 4.6 12.3 - - + -
172A MET* 4.2 32.5 - - + -
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Residues in contact with ARG 84 (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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80A CYS 3.0 18.1 + - - +
81A CYS* 3.7 4.9 - - - +
82A LEU 3.4 0.2 - - - -
83A LEU* 1.3 78.3 - - - +
85A HIS* 1.3 58.1 + - + +
87A LEU* 3.4 3.4 + - - +
88A ARG* 2.9 46.0 + - - +
120A LYS* 2.7 47.5 - - + +
123A LEU* 3.7 40.9 - - + +
124A ARG* 3.5 16.8 - - - +
127A HIS* 3.2 41.7 + - - +
132A CYS* 4.4 8.1 - - - -
178D GLU 5.1 5.5 + - - -
180D VAL* 4.2 8.9 - - - +
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Residues in contact with HIS 85 (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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81A CYS* 3.2 32.5 + - - -
82A LEU* 3.6 8.5 - - - +
83A LEU 3.2 0.4 - - - -
84A ARG* 1.3 74.8 - - + +
86A LEU* 1.3 56.5 + - - +
88A ARG* 3.1 29.8 + - - +
89A LEU* 2.7 34.3 + - - +
134A CYS* 3.9 10.5 - - - -
139A MET* 3.8 29.9 - - + -
142A TYR* 3.7 40.1 + + + -
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Residues in contact with LEU 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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65A LEU* 4.1 12.6 - - + -
71A LEU* 6.0 1.6 - - + -
82A LEU* 3.0 42.1 + - + +
83A LEU* 3.5 16.6 - - + +
85A HIS* 1.3 76.7 - - - +
87A LEU* 1.3 64.0 + - + +
89A LEU* 3.2 15.5 - - + +
90A TYR* 3.0 36.2 + - + -
142A TYR* 4.5 3.8 - - + -
145A ILE* 3.9 37.7 - - + -
168A LEU* 4.8 14.1 - - + -
171A TRP* 4.4 15.9 - - + -
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Residues in contact with LEU 87 (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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83A LEU* 2.9 32.1 + - + +
84A ARG* 3.7 5.2 - - - +
86A LEU* 1.3 74.1 - - + +
88A ARG* 1.3 67.7 + - - +
90A TYR* 3.2 5.7 + - + +
91A LEU* 2.8 37.4 + - + +
116A PHE* 3.3 45.1 - - + +
119A ILE* 3.5 39.0 - - + -
120A LYS* 3.8 12.1 - - + +
123A LEU* 4.0 7.9 - - + -
168A LEU* 4.5 11.0 - - + -
172A MET* 5.2 1.3 - - + -
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Residues in contact with ARG 88 (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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84A ARG* 2.9 52.7 + - - +
85A HIS* 3.1 34.5 + - - +
87A LEU* 1.3 74.3 - - - +
89A LEU* 1.3 56.7 + - - +
91A LEU* 4.5 7.4 - - - +
92A ASP* 2.7 64.3 + - + +
120A LYS* 4.1 20.8 - - - +
142A TYR* 5.4 3.4 - - - +
78B TYR* 6.0 0.4 - - - -
177D GLU* 5.8 7.7 - - - +
178D GLU* 5.4 7.7 + - - +
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Residues in contact with LEU 89 (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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64A ILE* 5.9 1.3 - - + -
85A HIS 2.7 16.9 + - - +
86A LEU* 3.2 16.4 - - + +
88A ARG* 1.3 75.2 - - - +
90A TYR* 1.3 65.2 + - + +
92A ASP* 4.8 0.7 - - - -
93A ARG* 3.0 59.7 + - + +
94A VAL* 3.8 5.0 + - + +
142A TYR* 3.8 28.7 - - + +
145A ILE* 4.3 18.8 - - + -
146A LEU* 4.3 11.0 - - + -
149A PHE* 4.3 31.2 - - + -
161A ALA* 6.5 1.1 - - + -
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Residues in contact with TYR 90 (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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64A ILE* 6.1 0.7 - - - +
65A LEU* 4.1 15.7 - - + +
86A LEU* 3.0 32.4 + - + +
87A LEU* 3.2 11.2 + - + +
89A LEU* 1.3 86.4 - - + +
91A LEU* 1.3 59.7 + - + +
94A VAL* 3.0 40.0 + - + -
95A PHE* 3.2 44.1 + + + -
116A PHE* 5.7 1.1 - + + -
161A ALA* 2.6 50.8 + - + +
162A LEU* 4.3 1.8 - - - -
164A GLU* 4.1 11.3 - - - +
165A LEU* 3.4 19.3 - - + -
168A LEU* 4.4 18.8 - - + -
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Residues in contact with LEU 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 LEU* 2.8 27.4 + - + +
88A ARG* 4.0 3.6 - - - +
90A TYR* 1.3 73.4 - - - +
92A ASP* 1.3 61.4 + - - +
95A PHE* 4.1 7.6 - - + -
96A LYS* 4.3 0.9 - - - +
113A ALA 3.6 24.2 - - - +
116A PHE* 4.1 18.4 - - + +
117A LEU* 4.2 10.1 - - + +
120A LYS* 3.8 33.0 - - + -
74B TYR* 2.8 41.6 + - + -
78B TYR* 3.4 35.0 - - + +
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Residues in contact with ASP 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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88A ARG* 2.7 52.5 + - + +
89A LEU* 4.1 1.8 - - - +
91A LEU* 1.3 73.4 - - - +
93A ARG* 1.3 72.5 + - + +
96A LYS* 3.4 25.8 + - - +
97A ASN* 4.6 0.2 + - - -
78B TYR* 3.2 25.2 + - - -
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Residues in contact with ARG 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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89A LEU* 3.0 29.8 + - + +
91A LEU 3.4 0.2 - - - -
92A ASP* 1.3 90.7 - - + +
94A VAL* 1.3 63.1 + - - +
96A LYS* 5.2 0.9 - - - -
97A ASN* 3.0 27.0 + - - +
142A TYR* 5.4 1.4 + - - -
146A LEU* 4.2 16.8 - - - +
149A PHE* 3.9 23.6 - - + -
150A GLU* 3.2 34.1 + - - +
158A VAL* 3.8 14.7 - - - +
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Residues in contact with VAL 94 (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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89A LEU* 4.0 6.3 - - + +
90A TYR* 3.0 44.5 + - + +
93A ARG* 1.3 80.7 - - - +
95A PHE* 1.3 70.2 + - - +
96A LYS 3.3 2.6 - - - +
97A ASN* 2.9 15.9 + - - +
98A TYR* 3.3 10.0 + - + +
149A PHE* 4.4 13.2 - - + -
158A VAL* 3.7 29.0 - - + +
161A ALA* 4.1 13.2 - - + -
162A LEU* 3.9 24.0 - - + +
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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