Contacts of the helix formed by residues 91 - 103 (chain A) in PDB entry 2AJA
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 91 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A THR 4.7 12.6 + - - +
59A ASN* 3.4 26.3 + - - +
62A GLN* 2.5 36.8 + - - +
89A GLY 3.8 1.0 + - - +
90A ILE* 1.3 82.9 - - - +
92A SER* 1.3 65.4 + - - +
93A GLU* 3.0 21.9 + - + +
94A VAL* 3.1 20.8 + - + +
95A ILE* 3.5 4.3 + - - +
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Residues in contact with SER 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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86A HIS* 3.5 26.9 + - - -
90A ILE 3.4 2.7 + - - -
91A LYS* 1.3 71.9 - - - +
93A GLU* 1.3 59.1 + - - +
95A ILE* 4.0 1.5 + - - -
96A CYS 3.8 1.4 + - - -
111A LEU* 3.1 37.0 - - - +
114A LEU* 5.4 0.2 - - - +
118A ASP* 5.5 2.0 + - - -
122A LYS* 3.1 38.6 + - - +
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Residues in contact with GLU 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ASN* 2.9 37.7 + - - +
91A LYS* 3.0 22.6 + - + +
92A SER* 1.3 77.0 - - - +
94A VAL* 1.3 64.0 + - - +
95A ILE 3.1 2.2 - - - -
96A CYS* 2.8 25.7 + - - +
97A PHE* 3.0 21.7 + - + -
122A LYS* 4.2 14.6 - - + +
126A ALA* 3.7 33.4 - - + +
127A GLU* 4.1 3.3 - - - +
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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
----------------------------------------------------------
59A ASN* 3.2 30.7 - - - +
62A GLN* 3.3 35.4 - - + +
63A VAL* 3.4 37.0 - - + +
66A LEU* 4.2 5.8 - - + -
90A ILE* 3.8 8.3 - - + -
91A LYS* 3.1 13.1 + - + +
93A GLU* 1.3 77.0 - - - +
95A ILE* 1.3 62.0 + - - +
97A PHE* 3.3 10.3 + - + +
98A VAL* 3.2 21.3 + - - +
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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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66A LEU* 3.7 13.9 - - + -
82A TRP* 3.6 34.5 - - + +
85A ALA* 4.0 4.9 - - + -
86A HIS* 4.0 20.2 - - + +
90A ILE* 3.6 20.4 - - + +
91A LYS 3.5 6.2 + - - +
92A SER* 4.1 2.0 - - - +
93A GLU 3.1 0.6 - - - -
94A VAL* 1.3 76.9 - - - +
96A CYS* 1.3 59.7 + - - +
98A VAL* 3.4 2.8 + - - +
99A ALA* 3.1 25.3 + - - +
107A ALA* 4.0 23.7 - - + +
111A LEU* 3.7 37.2 - - + -
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Residues in contact with CYS 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A SER 3.8 7.7 + - - +
93A GLU* 2.8 17.4 + - - +
95A ILE* 1.3 78.8 - - - +
97A PHE* 1.3 63.5 + - + +
99A ALA* 3.6 7.3 - - - +
100A ALA* 3.3 20.3 + - - +
108A LEU* 4.9 13.9 - - - -
111A LEU* 4.1 10.3 - - + -
122A LYS* 4.2 21.1 - - + +
131A ALA* 3.8 20.7 - - - +
143A VAL* 5.7 0.5 - - - +
147A LEU* 4.4 17.7 - - - -
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Residues in contact with PHE 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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59A ASN* 4.2 9.6 - - + -
63A VAL* 4.2 17.3 - - + -
93A GLU* 3.0 35.7 + - + -
94A VAL* 3.6 13.5 - - - +
95A ILE 3.2 0.2 - - - -
96A CYS* 1.3 78.3 - - - +
98A VAL* 1.3 57.0 + - - +
99A ALA 3.0 4.9 - - - -
100A ALA* 3.1 4.5 + - - +
101A ILE* 2.9 40.1 + - + +
122A LYS 5.0 2.0 - - - -
126A ALA* 3.7 38.1 - - + -
127A GLU* 3.8 16.8 - - + -
130A GLN* 3.7 24.9 - - + -
131A ALA* 4.0 25.8 - - + -
134A LEU* 4.0 12.1 - - + -
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Residues in contact with VAL 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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63A VAL* 4.4 11.9 - - + +
66A LEU* 3.4 31.6 - - + +
67A LEU* 3.5 35.2 - - + -
70A TYR* 5.0 1.1 - - + -
82A TRP* 3.9 24.9 - - + -
94A VAL* 3.2 15.2 + - + +
95A ILE 3.4 4.0 + - - +
97A PHE* 1.3 76.8 - - - +
99A ALA* 1.3 50.6 + - - +
101A ILE* 3.9 8.1 - - - -
102A THR* 2.4 42.9 + - + +
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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 ILE 3.1 16.1 + - - +
96A CYS* 3.6 11.7 - - - +
97A PHE 3.0 0.2 - - - -
98A VAL* 1.3 79.3 - - - +
100A ALA* 1.3 58.3 + - - +
101A ILE 3.2 0.4 - - - -
102A THR* 4.1 1.3 - - - -
103A GLY* 2.9 30.3 + - - -
104A CYS 3.5 13.4 + - - +
107A ALA* 3.8 19.5 - - + -
108A LEU* 4.4 18.8 - - + +
143A VAL* 3.6 8.6 - - + +
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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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96A CYS 3.3 10.7 + - - +
97A PHE 3.1 7.8 + - - +
99A ALA* 1.3 79.2 - - - +
101A ILE* 1.3 59.0 + - - +
131A ALA* 3.1 31.9 - - + +
134A LEU* 3.6 9.9 - - + +
135A ALA* 3.4 20.7 - - + +
140A HIS* 3.1 19.0 - - - -
143A VAL* 3.8 16.5 - - + +
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Residues in contact with ILE 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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25A LEU* 4.2 34.1 - - + -
29A LEU* 4.6 17.3 - - + -
63A VAL* 4.8 10.8 - - + -
67A LEU* 4.6 11.0 - - + -
71A TYR* 4.9 0.5 + - - -
97A PHE* 2.9 26.8 + - + +
98A VAL* 4.3 6.7 - - - +
100A ALA* 1.3 78.6 - - - +
102A THR* 1.3 58.9 + - + +
103A GLY 3.3 0.9 - - - -
134A LEU* 3.4 38.6 - - + -
138A ASN* 3.9 15.1 - - - +
140A HIS* 2.7 23.0 + - - -
209B ARG* 5.8 0.2 - - - +
238B LYS* 5.6 1.4 - - - -
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Residues in contact with THR 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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67A LEU* 3.9 8.3 - - + -
70A TYR* 3.5 40.3 + - + -
71A TYR* 3.3 25.6 - - + +
82A TRP* 5.0 0.2 - - - -
98A VAL* 2.4 36.0 + - + +
101A ILE* 1.3 76.4 - - - +
103A GLY* 1.3 62.6 + - - +
104A CYS* 3.2 18.7 + - - +
140A HIS* 3.7 7.4 + - - -
237B GLU* 4.4 7.1 - - - +
238B LYS* 4.7 6.8 - - - +
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Residues in contact with GLY 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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99A ALA 2.9 15.7 + - - -
101A ILE 3.3 3.0 - - - -
102A THR* 1.3 77.9 - - - +
104A CYS* 1.3 62.3 + - - +
105A SER* 3.3 2.1 + - - -
140A HIS* 3.7 24.0 - - - -
142A HIS* 2.6 28.8 + - - -
143A VAL* 3.9 2.5 - - - -
237B GLU* 3.5 11.3 - - - +
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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
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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