Contacts of the helix formed by residues 82 - 94 (chain A) in PDB entry 5IWM
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 GLY 82 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A HIS* 1.3 78.9 - - - +
83A ASP* 1.3 65.3 + - - -
84A SER* 3.3 4.0 - - - -
85A SER* 3.4 18.4 + - - -
86A ILE* 3.6 10.2 + - - +
122C ARG* 4.0 24.7 - - - +
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Residues in contact with ASP 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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71A VAL* 3.8 12.3 - - + +
75A MET* 3.5 32.9 - - + +
81A HIS 3.6 1.2 + - - -
82A GLY* 1.3 69.8 - - - -
84A SER* 1.3 61.1 + - - +
86A ILE* 3.3 3.8 + - - +
87A TYR* 2.9 30.9 + - - +
121A MET* 3.8 10.9 - - + +
122C ARG* 4.0 13.5 + - - +
101F 6EJ 2.5 61.5 + - - +
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Residues in contact with SER 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A GLY* 3.3 1.5 - - - -
83A ASP* 1.3 77.5 + - - +
85A SER* 1.3 65.7 + - - +
87A TYR* 4.5 4.9 - - - +
88A GLU* 3.0 46.9 + - - +
121A MET* 5.4 1.1 - - - -
101F 6EJ 3.9 23.0 - - - +
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Residues in contact with SER 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A VAL* 4.2 4.6 - - - +
79A HIS* 5.3 4.9 - - - -
81A HIS* 5.3 6.7 - - - -
82A GLY* 3.4 15.0 + - - -
83A ASP 3.3 0.4 - - - -
84A SER* 1.3 77.9 - - - +
86A ILE* 1.3 64.4 + - - +
88A GLU* 4.3 2.5 - - - +
89A ALA* 3.2 23.9 + - - +
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Residues in contact with ILE 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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45A VAL* 4.2 8.1 - - + -
49A ILE* 3.4 26.0 - - + +
70A ILE* 6.1 1.1 - - + -
71A VAL* 3.9 23.1 - - + +
74A VAL* 4.2 9.9 - - + -
75A MET* 3.7 38.8 - - + +
79A HIS* 3.6 33.2 - - + +
81A HIS 4.0 5.6 - - - +
82A GLY 3.6 14.3 + - - +
83A ASP* 3.3 7.5 + - - +
84A SER 3.2 0.2 - - - -
85A SER* 1.3 75.4 - - - +
87A TYR* 1.3 66.6 + - - +
89A ALA 3.3 1.4 + - - -
90A MET* 3.1 18.3 + - + +
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Residues in contact with TYR 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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67A SER* 3.8 9.2 - - - -
71A VAL* 4.0 15.7 - - + -
83A ASP 2.9 9.8 + - - +
84A SER* 4.1 3.8 - - - +
86A ILE* 1.3 76.0 - - - +
88A GLU* 1.3 65.7 + - + +
90A MET* 2.9 17.5 + - + +
91A VAL* 2.9 49.7 + - + +
110A PHE* 5.1 1.0 - + - -
118A ALA* 3.9 10.3 - - + +
119A ALA 2.6 29.6 + - - -
120A ALA* 4.4 1.3 - - - -
121A MET* 3.4 54.7 - - + -
124A THR* 2.7 30.0 + - - +
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Residues in contact with GLU 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 SER* 3.0 35.8 + - - +
85A SER* 4.5 2.4 - - - +
87A TYR* 1.3 83.7 - - + +
89A ALA* 1.3 55.9 - - - +
91A VAL* 3.5 11.9 + - + +
92A ARG* 3.2 32.7 + - - +
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Residues in contact with ALA 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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45A VAL* 4.0 20.0 - - + -
46A HIS* 3.7 24.2 - - + +
49A ILE* 4.0 1.8 - - + -
85A SER 3.2 19.5 + - - +
86A ILE 3.3 5.1 + - - +
87A TYR 3.1 0.6 - - - -
88A GLU* 1.3 75.2 - - - +
90A MET* 1.3 64.3 + - - +
92A ARG* 3.6 8.0 + - - +
93A MET* 3.5 26.9 + - - +
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Residues in contact with MET 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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49A ILE* 3.7 19.0 - - + +
53A LEU* 5.1 2.7 - - - -
67A SER* 3.3 34.3 - - - +
70A ILE* 3.8 34.8 - - - -
71A VAL* 5.3 3.1 - - + -
86A ILE* 3.1 12.0 + - + +
87A TYR* 2.9 26.9 + - + +
89A ALA* 1.3 74.4 - - - +
91A VAL* 1.3 64.3 + - - +
93A MET* 3.3 22.1 + - - +
94A ALA* 3.4 11.3 + - - +
104A VAL* 4.1 14.9 - - + +
110A PHE* 4.5 10.1 - - + -
126A ALA* 3.8 17.7 - - + -
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Residues in contact with VAL 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 TYR* 2.9 43.3 + - + +
88A GLU* 3.5 13.7 - - + +
90A MET* 1.3 76.3 - - + +
92A ARG* 1.3 62.7 + - + +
94A ALA* 3.1 15.4 + - - +
95A GLN* 3.4 20.4 - - - +
110A PHE* 3.7 37.6 - - + +
118A ALA* 3.7 31.2 - - + +
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Residues in contact with ARG 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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46A HIS* 5.3 6.3 + - - +
88A GLU 3.2 19.5 + - - +
89A ALA* 3.9 9.9 - - - +
90A MET 3.3 0.4 - - - -
91A VAL* 1.3 76.0 - - + +
93A MET* 1.3 57.7 - - - +
94A ALA 3.0 5.2 + - - -
95A GLN* 3.1 31.3 + - - +
98A SER* 3.5 27.1 + - - -
99A TYR* 3.3 39.0 + - + +
173A SER* 5.0 9.5 + - - -
266A PHE* 5.9 1.8 - - - -
267A GLN* 5.0 10.9 - - - +
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Residues in contact with MET 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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46A HIS* 3.6 28.5 - - + -
49A ILE* 3.7 35.7 - - + -
50A LEU* 4.1 18.8 - - + -
89A ALA 3.5 18.8 + - - +
90A MET* 3.3 13.5 + - - +
92A ARG* 1.3 77.4 - - - +
94A ALA* 1.3 56.6 + - - +
95A GLN 3.5 0.2 - - - -
99A TYR* 3.5 34.3 - - + +
102A PRO* 3.5 8.3 - - - +
103A LEU* 3.0 41.2 + - + -
104A VAL* 3.1 17.5 + - + -
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Residues in contact with ALA 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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90A MET 3.4 3.0 + - - +
91A VAL 3.1 12.0 + - - +
92A ARG 3.0 1.2 - - - -
93A MET* 1.3 78.6 - - - +
95A GLN* 1.3 60.0 + - - +
96A ASP* 3.8 1.9 + - - +
102A PRO* 4.6 5.4 - - - +
104A VAL* 3.2 37.9 - - + +
106A GLY* 4.3 9.1 + - - +
110A PHE* 3.9 24.9 - - + +
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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