Contacts of the helix formed by residues 72 - 85 (chain A) in PDB entry 3ISL
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 THR 72 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A GLY* 1.3 79.1 - - - +
73A SER* 1.3 67.0 + - - +
74A ARG* 3.7 1.0 + - - +
75A ALA 3.0 10.8 + - - -
76A GLY 3.1 7.4 + - - -
207A GLY* 4.3 16.6 - - - +
208A MET 4.6 0.4 - - - +
209A ALA* 3.4 2.3 - - - +
419A PLP 2.4 33.5 + - - -
70B ASP* 3.9 16.6 - - + +
250B TYR* 3.0 33.7 + - + +
268B HIS* 3.7 12.3 - - - +
269B THR 3.6 22.0 - - - +
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Residues in contact with SER 73 (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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72A THR* 1.3 75.8 - - - +
74A ARG* 1.3 58.4 + - - +
76A GLY* 2.9 5.9 + - - -
77A ILE* 2.9 27.9 + - - +
176A VAL* 3.4 28.9 - - - +
195A ILE* 3.7 3.6 - - - +
196A GLY 4.2 0.7 - - - -
197A GLY* 3.4 19.5 - - - -
198A THR 4.5 0.2 + - - -
199A GLN* 3.8 6.3 + - - -
208A MET 4.4 2.2 + - - -
209A ALA* 3.6 12.8 - - - +
419A PLP 2.8 28.1 + - - -
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Residues in contact with ARG 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A THR* 3.1 0.8 - - - +
73A SER* 1.3 75.9 - - - +
75A ALA* 1.3 61.3 + - - +
77A ILE* 3.7 12.9 - - + +
78A GLU* 3.0 27.5 + - - +
99A PHE* 4.0 11.9 - - - -
102A LEU* 3.9 47.2 - - + +
106A ILE* 4.3 4.0 - - + +
419A PLP 2.9 55.1 + - + +
249B ASN* 4.2 10.3 - - - +
250B TYR* 3.7 16.8 - - + -
266B ASN* 4.1 14.8 + - - +
267B HIS* 2.7 36.3 + - - +
268B HIS* 3.7 9.7 - - - +
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Residues in contact with ALA 75 (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 ILE* 3.6 2.5 - - + -
71A GLY* 3.8 10.1 - - - -
72A THR 3.0 10.6 + - - +
74A ARG* 1.3 78.5 - - - +
76A GLY* 1.3 60.8 + - - +
78A GLU* 3.8 1.5 - - - +
79A ALA* 2.9 30.5 + - - +
251A PHE* 3.4 35.6 - - + -
250B TYR* 3.5 28.1 - - + -
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Residues in contact with GLY 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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69A ILE* 3.5 23.2 - - - +
72A THR 3.1 6.7 + - - -
73A SER 2.9 9.1 + - - -
75A ALA* 1.3 78.0 - - - +
77A ILE* 1.3 60.5 + - - +
79A ALA* 3.4 2.5 + - - +
80A VAL* 3.2 28.1 + - - +
195A ILE* 3.9 9.0 - - - -
209A ALA* 3.7 9.2 - - - -
211A ILE* 4.3 3.9 - - - +
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Residues in contact with ILE 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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73A SER 2.9 14.5 + - - +
74A ARG* 3.7 19.5 - - + +
75A ALA 3.3 0.2 - - - -
76A GLY* 1.3 76.6 - - - +
78A GLU* 1.3 57.8 + - - +
80A VAL* 3.4 3.3 + - - +
81A LEU* 2.9 39.4 + - + +
102A LEU* 4.8 5.6 - - + -
103A LEU* 3.6 27.1 - - + -
106A ILE* 4.0 10.3 - - + -
172A ILE* 6.1 0.2 - - + -
174A ASP* 3.5 34.8 - - + +
176A VAL* 4.3 4.5 - - + -
195A ILE* 3.9 31.4 - - + +
419A PLP 4.3 10.5 - - + +
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Residues in contact with GLU 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 ARG 3.0 19.0 + - - +
75A ALA* 3.8 6.7 - - - +
76A GLY 3.3 0.2 - - - -
77A ILE* 1.3 73.8 - - - +
79A ALA* 1.3 56.0 + - - +
81A LEU* 4.0 0.3 - - - +
82A ALA* 2.6 38.5 + - - +
106A ILE* 4.0 19.9 - - + +
110A TYR* 2.8 36.6 + - + +
251A PHE* 4.0 11.2 - - + -
248B SER* 2.6 32.5 + - - -
249B ASN* 3.5 12.0 + - - +
250B TYR* 3.0 27.4 + - - +
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Residues in contact with ALA 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ILE* 4.7 7.6 - - + -
75A ALA 2.9 16.4 + - - +
76A GLY* 3.9 6.3 - - - +
77A ILE 3.4 0.2 - - - -
78A GLU* 1.3 75.0 - - - +
80A VAL* 1.3 64.6 + - - +
82A ALA* 3.8 0.4 - - - +
83A SER* 3.1 25.8 + - - -
251A PHE* 3.3 46.4 - - + +
253A LEU* 3.8 17.2 - - + +
256A LEU* 5.5 0.2 - - + -
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Residues in contact with VAL 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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76A GLY 3.2 15.2 + - - +
77A ILE 3.8 6.3 - - - +
79A ALA* 1.3 74.5 - - - +
81A LEU* 1.3 62.5 + - - +
83A SER* 2.8 19.7 + - - +
84A VAL* 3.3 8.6 + - + +
172A ILE* 3.8 31.4 - - + -
193A ALA* 3.8 19.5 - - + -
194A ALA 5.4 0.4 - - - +
195A ILE* 3.7 19.5 - - + -
211A ILE* 4.2 17.3 - - + -
212A THR 5.8 0.2 - - - +
213A TYR* 5.2 3.1 - - + -
217A VAL* 5.3 6.5 - - + -
253A LEU* 3.8 21.3 - - + -
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Residues in contact with LEU 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 ILE* 2.9 34.8 + - + +
80A VAL* 1.3 74.8 - - - +
82A ALA* 1.3 63.1 + - - +
84A VAL* 3.3 3.3 + - + -
85A ILE* 3.1 50.3 + - + +
91A VAL* 5.6 0.7 - - + -
103A LEU* 4.3 21.3 - - + +
106A ILE* 3.7 32.8 - - + -
107A ALA* 4.8 4.3 - - + +
110A TYR* 5.1 0.9 - - - -
141A ILE* 4.6 4.3 - - + -
143A ALA* 4.4 14.4 - - + -
172A ILE* 4.2 33.2 - - + -
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Residues in contact with ALA 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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78A GLU 2.6 23.1 + - - +
79A ALA* 3.8 6.7 - - - +
81A LEU* 1.3 73.7 - - - +
83A SER* 1.3 61.3 + - - +
85A ILE 3.7 4.5 - - - +
110A TYR* 3.7 44.2 - - + +
224A ARG* 3.1 16.6 + - - -
246A ILE* 3.8 22.1 - - + +
247A THR 5.1 0.2 + - - -
248A SER* 5.0 0.7 - - - -
251A PHE* 4.8 4.9 - - + -
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Residues in contact with SER 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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79A ALA 3.1 13.5 + - - -
80A VAL* 2.8 18.9 + - - +
82A ALA* 1.3 78.1 - - - +
84A VAL* 1.3 60.4 + - - +
217A VAL* 5.4 0.2 - - - +
220A VAL* 4.5 0.7 - - - +
221A ILE* 3.7 18.6 - - - +
224A ARG* 3.2 23.6 + - - -
246A ILE* 3.3 28.8 - - - +
251A PHE 4.6 1.3 - - - -
253A LEU* 3.4 29.5 - - - +
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Residues in contact with VAL 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 VAL* 3.7 11.4 - - + +
81A LEU* 3.3 6.4 + - + +
82A ALA 3.2 0.2 - - - -
83A SER* 1.3 84.7 + - - +
85A ILE* 1.3 57.1 + - + +
140A LYS* 3.1 29.2 + - - -
141A ILE* 3.3 26.6 - - + +
170A LEU* 4.0 11.9 - - + -
172A ILE* 3.7 23.6 - - + -
217A VAL* 3.9 29.2 - - + +
220A VAL* 3.9 22.4 - - + -
221A ILE* 4.5 1.3 - - + -
224A ARG* 4.0 2.0 - - - -
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Residues in contact with ILE 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 LEU* 3.1 36.8 + - + +
82A ALA 3.7 4.5 - - - +
84A VAL* 1.3 76.9 - - + +
86A GLU* 1.3 71.0 + - - +
87A PRO* 4.8 0.5 - - - +
89A ASP* 3.7 4.3 - - + +
91A VAL* 4.0 11.4 - - + -
107A ALA* 3.9 33.0 - - + +
110A TYR* 3.7 30.5 - - + +
112A ALA* 3.8 17.3 - - + +
141A ILE* 3.5 21.5 - - + -
224A ARG* 2.8 22.7 + - - +
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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