Contacts of the helix formed by residues 86 - 104 (chain A) in PDB entry 1HZ4
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 VAL 86 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A PHE* 4.2 5.8 - - + -
48A TYR* 3.6 36.6 - - + -
51A ILE* 3.8 21.8 - - + -
81A ALA* 2.8 22.5 + - - +
84A HIS* 3.5 19.1 - - + +
85A ASP* 1.3 72.6 - - - +
87A TRP* 1.3 64.4 + - - +
88A HIS* 3.3 20.0 - - + +
89A TYR* 4.0 15.9 - - + -
90A ALA* 3.2 15.4 + - - +
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Residues in contact with TRP 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ARG* 4.2 25.6 - - + -
85A ASP* 3.1 57.1 + - - +
86A VAL* 1.3 73.7 - - - +
88A HIS* 1.3 58.6 + - - +
90A ALA* 3.2 8.5 + - + +
91A LEU* 2.9 31.4 + - - +
120A LEU* 3.8 26.3 - - + +
124A GLN* 3.4 48.9 + - + -
126A LEU* 3.9 24.6 - - + +
784A BEZ 4.0 9.4 - + + -
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Residues in contact with HIS 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A TYR* 2.9 26.8 + + - -
86A VAL* 3.7 20.9 - - + +
87A TRP* 1.3 79.2 + - - +
89A TYR* 1.3 81.9 + + - +
91A LEU* 4.6 0.2 - - - -
92A TRP* 3.0 29.5 + - - +
131A MET* 3.5 13.3 - - + +
784A BEZ 3.5 45.3 - + + -
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Residues in contact with TYR 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 5.2 2.4 - - - +
20A GLN* 2.7 37.8 + - - +
48A TYR* 3.4 22.7 - + - -
51A ILE* 3.7 24.5 - - + -
52A VAL* 3.6 23.8 - - + +
55A SER* 3.5 33.4 - - - -
77A THR* 4.4 4.4 - - + +
81A ALA* 4.0 4.3 - - + -
86A VAL* 3.2 15.6 + - + +
88A HIS* 1.3 100.6 - + - +
90A ALA* 1.3 60.8 + - - +
92A TRP* 3.9 14.4 - + - +
93A SER* 3.0 29.1 + - - -
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Residues in contact with ALA 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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78A GLU* 4.2 9.1 - - + +
81A ALA* 3.6 18.3 - - + +
82A ARG* 4.2 21.3 - - + +
86A VAL 3.2 7.9 + - - +
87A TRP* 3.2 13.2 + - + +
89A TYR* 1.3 78.1 - - - +
91A LEU* 1.3 61.3 + - - +
93A SER* 3.3 7.0 + - - -
94A LEU* 3.1 26.5 + - - +
120A LEU* 3.9 16.6 - - + -
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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
----------------------------------------------------------
87A TRP 2.9 16.6 + - - +
88A HIS 4.5 0.2 - - - -
90A ALA* 1.3 75.6 - - - +
92A TRP* 1.3 65.2 + - - +
94A LEU* 3.2 4.3 + - - +
95A ILE* 3.0 36.5 + - + +
117A ALA* 3.7 29.6 - - + +
120A LEU* 3.8 11.4 - - + +
121A ILE* 4.1 35.0 - - + -
126A LEU* 4.6 4.3 - - + +
131A MET* 3.6 39.5 - - + -
132A HIS 4.7 0.9 - - - +
135A LEU* 4.5 1.8 - - + -
784A BEZ 4.1 15.3 - - + -
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Residues in contact with TRP 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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20A GLN* 5.0 3.0 - - - +
24A ASN* 6.0 1.1 - - - -
55A SER* 3.9 13.6 + - - -
59A GLU* 3.2 32.5 + - - -
88A HIS 3.0 19.7 + - - +
89A TYR* 3.9 18.2 - + - +
91A LEU* 1.3 75.4 - - - +
93A SER* 1.3 62.4 + - - +
95A ILE* 3.3 22.6 + - + -
96A GLN* 3.0 63.0 + - + +
99A GLU* 4.8 3.8 - - - -
131A MET* 3.6 18.8 - - + -
134A PHE* 3.7 35.2 - + - -
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Residues in contact with SER 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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55A SER* 5.9 0.2 - - - -
74A MET* 2.7 33.6 + - - +
77A THR* 4.6 6.1 - - - -
78A GLU* 3.5 13.4 - - - +
89A TYR 3.0 19.4 + - - -
90A ALA 3.4 6.1 - - - -
91A LEU 3.2 0.2 - - - -
92A TRP* 1.3 77.2 - - - +
94A LEU* 1.3 57.3 + - - +
96A GLN* 3.2 14.5 + - - +
97A GLN* 2.9 40.5 + - - +
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Residues in contact with LEU 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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78A GLU* 3.5 28.9 - - - +
82A ARG* 3.9 21.1 - - - +
90A ALA 3.1 15.0 + - - +
91A LEU* 3.2 6.5 + - - +
93A SER* 1.3 79.3 - - - +
95A ILE* 1.3 62.3 + - - +
97A GLN* 3.3 9.3 + - - +
98A SER* 3.0 20.8 + - - -
113A THR* 3.5 26.9 - - + +
114A GLN* 6.3 0.2 - - - -
116A LYS* 4.1 19.3 - - + +
117A ALA* 3.8 38.1 - - + +
120A LEU* 4.3 10.5 - - + -
135A LEU* 6.3 0.2 - - - -
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Residues in contact with ILE 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 LEU* 3.0 29.1 + - + +
92A TRP* 3.6 21.5 - - + +
94A LEU* 1.3 75.9 - - - +
96A GLN* 1.3 63.3 + - - +
98A SER* 3.2 5.6 + - - -
99A GLU* 3.0 22.6 + - + +
117A ALA* 5.3 0.4 - - + -
131A MET* 3.6 42.4 - - + +
134A PHE* 3.5 41.3 - - + -
135A LEU* 4.2 22.7 - - + +
138A ILE* 3.8 11.1 - - + +
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Residues in contact with GLN 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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55A SER* 4.1 9.7 + - - +
59A GLU* 3.3 25.1 + - - +
62A HIS* 4.7 3.1 + - - +
74A MET* 3.5 31.6 - - + +
92A TRP* 3.0 75.6 + - + +
93A SER* 3.6 11.0 - - - +
95A ILE* 1.3 73.6 - - - +
97A GLN* 1.3 67.0 + - - +
99A GLU* 3.2 17.1 + - - +
100A ILE* 3.1 25.5 + - - +
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Residues in contact with GLN 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A LEU* 3.9 15.9 - - + +
74A MET* 3.8 30.1 + - + -
75A GLN* 4.2 18.1 + - + +
78A GLU* 3.0 26.1 + - - +
93A SER* 2.9 40.1 + - - +
94A LEU* 3.6 15.4 - - - +
95A ILE 3.3 0.2 - - - -
96A GLN* 1.3 76.0 - - - +
98A SER* 1.3 63.9 + - - +
100A ILE* 3.3 4.2 + - - +
101A LEU* 3.0 30.6 + - + +
113A THR* 3.9 11.1 - - + +
116A LYS* 5.4 4.2 + - - -
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Residues in contact with SER 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 LEU 3.0 12.7 + - - -
95A ILE 3.5 8.3 - - - -
97A GLN* 1.3 78.2 - - - +
99A GLU* 1.3 64.5 + - - +
101A LEU* 3.0 12.1 + - - +
102A PHE* 2.8 25.4 + - - +
110A ALA* 3.7 11.5 + - - +
113A THR* 4.0 5.3 - - - +
114A GLN* 2.9 37.9 + - - +
138A ILE* 3.6 13.0 - - - +
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Residues in contact with GLU 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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62A HIS* 4.0 20.2 + - + -
92A TRP* 4.8 3.6 - - - -
95A ILE* 3.0 18.2 + - - +
96A GLN* 3.2 24.9 + - - +
98A SER* 1.3 78.4 + - - +
100A ILE* 1.3 61.9 + - - +
102A PHE* 3.5 6.2 + - - +
103A ALA* 3.1 23.6 + - - +
134A PHE* 3.5 29.6 - - + -
138A ILE* 4.6 17.0 - - + +
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Residues in contact with ILE 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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62A HIS* 3.6 30.3 - - + +
67A LEU* 4.0 17.5 - - + +
70A SER* 3.6 20.6 - - - +
71A LEU* 3.9 26.5 - - + -
74A MET* 3.4 26.2 - - + -
96A GLN 3.1 5.8 + - - +
97A GLN 3.8 6.5 - - - +
98A SER 3.2 0.4 - - - -
99A GLU* 1.3 77.0 - - - +
101A LEU* 1.3 65.1 + - - +
103A ALA* 3.1 8.2 + - - +
104A GLN* 2.9 47.1 + - + +
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Residues in contact with LEU 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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71A LEU* 4.8 13.7 - - + -
97A GLN* 3.0 22.9 + - + +
98A SER 3.0 6.3 + - - +
100A ILE* 1.3 74.6 - - - +
102A PHE* 1.3 62.3 + - - +
104A GLN* 3.2 24.1 + - - +
106A PHE* 3.0 41.1 + - + +
109A THR* 3.7 28.9 - - + +
110A ALA* 4.0 10.5 - - + -
113A THR* 3.2 31.0 - - + +
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Residues in contact with PHE 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 SER* 2.8 21.6 + - - +
99A GLU* 3.8 6.1 - - - +
101A LEU* 1.3 72.6 - - - +
103A ALA* 1.3 58.7 + - - +
105A GLY* 2.9 6.4 + - - -
107A LEU* 3.6 37.3 - - + +
110A ALA* 4.0 8.7 - - + +
114A GLN* 5.8 1.8 - - - +
138A ILE 5.7 0.4 - - - -
141A GLN* 3.6 37.5 - - + +
142A LEU* 3.9 28.5 - - + -
145A ALA* 4.4 6.5 - - + -
288A SER* 2.6 33.9 + - - -
292A ARG* 3.4 28.7 - - - -
326A PHE* 4.2 15.7 - + - -
775A SO4 4.9 3.4 - - - -
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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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62A HIS* 5.9 2.9 - - - +
67A LEU* 5.6 1.6 - - + -
99A GLU 3.1 14.5 + - - +
100A ILE* 3.1 10.5 + - - +
102A PHE* 1.3 79.7 - - - +
104A GLN* 1.3 62.1 + - + +
105A GLY 3.3 0.9 + - - -
248A HIS* 5.8 4.3 - - + -
286A LEU* 3.4 38.5 - - + +
288A SER* 3.4 17.0 + - - -
289A ASP* 4.4 5.1 + - - +
292A ARG* 6.1 0.7 - - - +
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Residues in contact with GLN 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LEU* 3.9 28.8 - - + +
68A THR* 5.1 5.3 + - - +
71A LEU* 4.3 8.9 - - - +
100A ILE* 2.9 38.8 + - + +
101A LEU* 3.6 13.5 - - - +
102A PHE 3.1 0.4 - - - -
103A ALA* 1.3 76.2 - - - +
105A GLY* 1.3 59.4 + - - +
106A PHE* 3.5 45.3 + - + -
284A LEU 5.2 2.5 + - - +
285A ARG* 3.7 17.4 - - + +
286A LEU* 4.5 1.3 - - + +
287A MET* 3.6 21.3 - - - +
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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