Contacts of the helix formed by residues 88 - 100 (chain A) in PDB entry 1HVD
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 88 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A ASN* 2.8 36.4 + - - +
86A LYS 3.3 3.4 + - - -
87A PRO* 1.3 69.7 - - - +
89A ARG* 1.3 60.5 + - - +
90A LEU 3.3 0.9 + - - -
91A TYR* 3.6 15.8 + - - +
92A ASP* 4.7 3.5 + - - +
278A GLU* 4.8 6.6 + - - +
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Residues in contact with ARG 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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87A PRO* 3.0 9.2 + - + -
88A SER* 1.3 78.4 - - - +
90A LEU* 1.3 80.4 + - + +
92A ASP 5.4 0.6 + - - -
93A ALA* 5.1 1.6 + - - +
125A ILE* 5.7 5.4 - - - +
127A GLN* 5.0 8.1 + - - -
128A VAL* 3.5 45.4 - - + +
131A GLU* 3.3 26.1 + - - -
132A GLU* 5.1 1.0 + - - -
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Residues in contact with LEU 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LYS* 4.7 17.3 - - + +
87A PRO* 2.9 39.0 + - + +
89A ARG* 1.3 97.9 - - + +
91A TYR* 1.3 61.5 + - - +
92A ASP 3.6 1.3 - - - -
93A ALA* 3.2 7.9 + - - +
94A TYR* 2.9 27.6 + - + +
128A VAL* 3.4 28.0 - - + -
132A GLU* 3.8 28.9 - - + +
133A TYR* 5.1 1.2 + - - +
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Residues in contact with TYR 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ALA* 3.8 35.7 - - + +
86A LYS* 3.8 24.7 - - + +
87A PRO 3.3 11.8 + - - +
88A SER* 3.6 11.9 + - - +
90A LEU* 1.3 77.4 - - - +
92A ASP* 1.3 65.0 + - - +
94A TYR* 3.1 25.5 + + - +
95A GLU* 3.0 44.3 + - + +
267A HIS* 5.6 0.5 + - - -
270A ILE* 4.3 2.6 + - - +
271A ARG* 3.5 40.9 + - + +
274A VAL* 4.2 7.2 - - + -
275A SER* 3.9 26.0 - - - -
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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
----------------------------------------------------------
88A SER 4.7 4.4 + - - +
89A ARG 5.4 0.8 + - - -
90A LEU 3.6 0.4 - - - -
91A TYR* 1.3 78.7 - - - +
93A ALA* 1.3 57.6 + - - +
95A GLU* 3.4 4.7 + - - +
96A LEU* 2.9 34.3 + - - +
113A ILE* 3.9 16.7 - - + +
117A ARG* 3.0 44.5 + - - +
121A GLU* 5.6 1.2 - - - +
125A ILE* 3.7 28.9 - - + +
271A ARG* 5.7 0.7 - - - +
275A SER* 3.9 12.8 - - - -
276A ARG* 5.1 0.3 + - - -
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Residues in contact with ALA 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 ARG 5.1 1.3 + - - +
90A LEU 3.2 11.5 + - - +
92A ASP* 1.3 77.8 - - - +
94A TYR* 1.3 57.3 + - - +
96A LEU* 3.4 3.5 + - - -
97A LYS* 3.0 30.3 + - - +
125A ILE* 4.3 15.6 - - + +
128A VAL* 4.4 10.8 - - + -
129A TYR* 3.6 42.0 - - + +
133A TYR* 3.7 6.9 - - + -
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Residues in contact with TYR 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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82A VAL* 5.3 10.1 - - + +
83A ALA* 6.4 0.7 - - - -
86A LYS* 3.5 38.6 - - + +
90A LEU* 2.9 14.5 + - + +
91A TYR* 3.2 29.2 - + - +
93A ALA* 1.3 77.8 - - - +
95A GLU* 1.3 79.2 + - - +
97A LYS* 3.5 0.7 + - - +
98A HIS* 2.9 69.2 + + - -
133A TYR* 3.4 18.6 + - - +
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Residues in contact with GLU 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 TYR* 3.0 43.3 + - + +
92A ASP* 3.4 8.0 + - - +
94A TYR* 1.3 90.2 - - + +
96A LEU* 1.3 60.2 + - - +
98A HIS* 3.4 6.7 + - - +
99A ALA* 3.1 22.7 + - - +
109A VAL* 3.9 10.7 - - + +
113A ILE* 3.8 15.7 - - + -
267A HIS* 3.0 38.4 + - - -
271A ARG* 3.1 28.2 + - - -
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Residues in contact with LEU 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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92A ASP 2.9 22.4 + - - +
93A ALA 3.6 5.6 - - - +
94A TYR 3.3 0.2 - - - -
95A GLU* 1.3 75.0 - - - +
97A LYS* 1.3 62.6 + - - +
99A ALA* 3.1 14.0 + - - +
100A LEU* 3.1 18.8 + - - +
109A VAL* 4.5 1.3 - - + +
110A LEU* 4.1 28.7 - - + +
113A ILE* 3.7 39.5 - - + -
114A ILE* 4.8 12.3 - - + -
122A LEU* 6.2 0.7 - - + -
125A ILE* 3.8 24.9 - - + -
129A TYR* 4.1 11.2 - - + -
137A LEU* 4.0 21.1 - - + -
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Residues in contact with LYS 97 (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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93A ALA 3.0 17.6 + - - +
94A TYR 3.7 4.9 - - - +
96A LEU* 1.3 73.5 - - - +
98A HIS* 1.3 65.5 + - + +
100A LEU* 3.2 1.9 + - - +
101A LYS* 3.0 63.4 + - + +
129A TYR* 3.3 23.6 + - + +
133A TYR* 3.7 46.8 + - + +
135A SER* 5.9 1.4 - - - -
140A ASP* 3.9 17.6 + - - -
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Residues in contact with HIS 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 TYR* 2.9 65.9 + + + +
95A GLU* 3.4 9.4 + - - +
96A LEU 3.3 0.2 - - - -
97A LYS* 1.3 87.9 - - + +
99A ALA* 1.3 58.9 + - - +
101A LYS* 4.4 21.0 + - + +
106A ASN* 5.4 0.2 - - - +
133A TYR* 5.1 3.6 - + - -
267A HIS* 5.8 5.2 - - - +
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Residues in contact with ALA 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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95A GLU 3.1 12.3 + - - +
96A LEU 3.1 9.0 + - - +
98A HIS* 1.3 75.1 - - - +
100A LEU* 1.3 62.2 + - - +
101A LYS 4.3 1.8 - - - +
105A THR* 3.2 10.9 + - - +
106A ASN* 2.8 57.9 + - + +
109A VAL* 3.9 13.2 - - + -
110A LEU* 3.7 12.3 - - + -
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Residues in contact with LEU 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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96A LEU 3.1 15.8 + - - +
97A LYS* 3.8 4.5 - - + +
99A ALA* 1.3 77.2 - - - +
101A LYS* 1.3 58.8 + - - +
105A THR* 3.2 2.2 + - - +
110A LEU* 4.0 29.6 - - + -
129A TYR* 3.6 22.4 - - - +
137A LEU* 4.1 19.7 - - + -
140A ASP* 3.9 23.3 - - + +
141A VAL* 4.2 11.7 - - + -
144A ASP* 2.9 37.7 - - + +
600A CA 2.1 33.4 - - - -
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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