Contacts of the helix formed by residues 84 - 101 (chain A) in PDB entry 2WWA
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 LEU 84 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A VAL 5.0 5.2 - - - +
72A PHE* 2.9 17.1 + - - +
83A GLY* 1.4 72.6 - - - -
85A PHE* 1.4 57.2 + - - +
86A PRO* 3.5 2.5 - - - -
87A ASN* 3.1 22.9 + - + +
88A ILE* 2.9 35.7 + - + +
164A THR* 4.9 13.0 - - + +
165A THR* 6.1 0.9 - - + -
168A ALA* 5.1 4.0 - - + -
180A GLY 4.7 1.1 - - - +
181A ALA* 3.3 44.0 - - + +
184A ILE* 3.5 28.3 - - + -
185A ASN* 4.7 13.5 - - - +
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Residues in contact with PHE 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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71A VAL* 4.6 6.3 - - + -
72A PHE* 3.3 55.2 + + + +
82A PHE 3.1 17.6 + - - +
84A LEU* 1.4 75.7 - - - +
86A PRO* 1.3 65.1 - - + +
88A ILE* 3.4 8.4 - - + +
89A SER* 3.3 21.5 + - - -
131A LEU* 3.8 17.5 - - + -
301A THR* 3.8 25.8 - - + -
304A PHE* 3.4 26.0 - - + -
305A TYR* 3.2 49.3 + + - -
312A VAL* 4.6 4.5 - - + -
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Residues in contact with PRO 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A PHE* 4.3 2.9 - - + -
83A GLY 3.9 7.2 - - - +
84A LEU 3.6 1.3 - - - -
85A PHE* 1.3 93.7 - - + +
87A ASN* 1.4 59.1 + - - +
89A SER* 3.6 2.3 - - - -
90A SER* 3.1 27.2 + - - -
124A ALA* 3.6 16.8 - - - +
127A GLN* 3.6 31.1 - - + +
128A TYR* 3.3 40.2 - - + -
131A LEU* 3.6 16.4 - - + -
305A TYR* 3.9 1.3 - - - +
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Residues in contact with ASN 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LEU* 3.1 29.0 + - + +
86A PRO* 1.4 77.7 - - - +
88A ILE* 1.4 61.5 + - - +
90A SER* 3.0 18.3 + - - -
91A GLY* 3.6 5.2 + - - -
120A THR* 4.4 8.1 - - - +
121A LYS* 5.2 4.3 - - - +
124A ALA* 3.6 19.2 - - - +
165A THR* 3.7 29.1 - - + +
168A ALA* 4.6 12.9 - - - +
181A ALA* 5.4 5.5 - - - +
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Residues in contact with ILE 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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71A VAL* 5.6 4.0 - - + +
84A LEU* 2.9 24.9 + - + +
85A PHE* 3.4 16.4 - - + +
87A ASN* 1.4 77.0 - - - +
89A SER* 1.4 59.7 + - - +
91A GLY* 3.0 6.7 + - - -
92A LEU* 3.0 36.9 + - + +
294A LEU* 6.6 0.2 - - + -
297A LEU* 4.5 20.6 - - + +
298A PHE* 3.8 25.6 - - + -
301A THR* 3.7 31.0 - - + +
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Residues in contact with SER 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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85A PHE 3.3 16.7 + - - -
86A PRO* 3.6 7.0 - - - -
87A ASN 3.3 0.4 - - - -
88A ILE* 1.4 77.3 - - - +
90A SER* 1.4 55.5 + - - +
91A GLY 3.1 4.7 - - - -
92A LEU* 3.1 14.0 + - - +
93A ILE* 3.0 34.0 + - - +
127A GLN* 3.9 12.8 + - - -
305A TYR* 3.2 37.9 + - - -
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Residues in contact with SER 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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86A PRO 3.1 14.0 + - - -
87A ASN 3.0 16.6 + - - -
89A SER* 1.4 73.5 - - - +
91A GLY* 1.4 58.1 + - - +
93A ILE* 4.1 10.8 - - - -
94A LEU* 3.3 32.9 + - - +
120A THR* 3.0 32.1 + - - +
123A PHE* 3.7 26.0 - - - -
124A ALA* 3.6 5.2 - - - +
127A GLN* 5.1 0.6 - - - +
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Residues in contact with GLY 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 ASN 3.6 3.4 + - - -
88A ILE* 3.0 13.2 + - - -
90A SER* 1.4 79.7 + - - +
92A LEU* 1.4 56.7 + - - +
94A LEU* 3.6 1.4 + - - +
95A GLN* 3.0 32.8 + - - +
116A PHE* 5.4 3.7 - - - -
120A THR* 4.2 8.7 - - - +
298A PHE* 4.4 13.9 - - - -
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Residues in contact with LEU 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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88A ILE* 3.0 33.9 + - + +
89A SER* 3.1 10.7 + - - +
91A GLY* 1.4 72.0 - - - +
93A ILE* 1.4 61.9 + - + +
95A GLN* 3.5 5.5 + - - +
96A LEU* 3.0 29.6 + - - +
298A PHE* 3.7 48.5 - - + +
301A THR* 3.7 31.2 - - + -
302A ILE* 3.7 29.4 - - + -
305A TYR* 5.0 5.2 - - + -
381A PHE* 4.4 10.3 - - + -
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Residues in contact with ILE 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 SER* 3.0 27.5 + - - +
90A SER* 4.2 10.5 - - - +
91A GLY 3.4 0.2 - - - -
92A LEU* 1.4 76.2 - - + +
94A LEU* 1.4 72.3 + - + +
96A LEU* 3.5 9.8 + - - +
97A LEU* 3.1 35.2 + - + +
123A PHE* 4.7 18.8 - - + +
127A GLN* 3.7 24.2 - - + +
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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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90A SER 3.3 21.5 + - - +
91A GLY 4.5 0.7 - - - +
92A LEU 3.3 0.2 - - - -
93A ILE* 1.4 82.5 - - + +
95A GLN* 1.4 59.8 + - - +
96A LEU 3.3 0.9 - - - -
97A LEU* 4.0 26.2 - - + +
98A ALA* 3.3 27.2 + - - +
116A PHE* 3.4 29.3 - - + +
119A LEU* 3.6 37.7 - - + +
120A THR* 3.5 29.2 - - - +
123A PHE* 4.6 10.5 - - + -
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Residues in contact with GLN 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 GLY 3.0 20.0 + - - +
92A LEU* 3.7 7.2 - - - +
94A LEU* 1.4 76.7 - - - +
96A LEU* 1.4 57.3 + - - +
99A GLY* 3.1 26.3 + - - -
116A PHE* 4.9 8.5 - - - -
298A PHE* 3.7 26.7 - - + -
381A PHE* 3.8 26.2 - - + +
384A LYS* 3.3 36.2 - - + +
385A TRP* 3.4 20.5 + - - -
388A ILE* 3.7 22.4 - - - +
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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 LEU 3.0 18.1 + - - +
93A ILE* 3.5 9.0 - - - +
94A LEU 3.3 0.2 - - - -
95A GLN* 1.4 75.8 - - - +
97A LEU* 1.4 65.5 + - + +
100A LEU* 3.0 47.5 + - + +
302A ILE* 6.3 2.9 - - + -
380A TRP* 3.7 38.6 - - + +
381A PHE* 5.0 7.2 - - + -
384A LYS* 5.3 0.9 - - - -
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Residues in contact with LEU 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 ILE* 3.1 26.0 + - + +
94A LEU* 4.0 26.7 - - + +
95A GLN 3.6 0.4 - - - -
96A LEU* 1.4 80.3 - - + +
98A ALA* 1.4 60.5 + - - +
100A LEU* 6.1 0.7 - - + -
101A LYS 3.4 6.1 + - - -
102A VAL* 3.4 25.5 - - + +
103A ILE* 3.1 52.5 + - + +
123A PHE* 6.1 1.6 - - + -
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Residues in contact with ALA 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 3.3 18.7 + - - +
97A LEU* 1.4 78.7 - - - +
99A GLY* 1.4 60.2 + - - +
101A LYS* 3.6 13.3 - - - +
103A ILE* 3.4 20.3 - - - +
104A LYS* 5.0 1.6 - - - -
105A VAL* 5.5 7.3 + - + +
107A PHE* 4.2 19.0 - - + -
116A PHE* 4.3 5.2 - - + -
387A ALA* 5.8 0.3 - - - +
388A ILE* 3.6 22.8 - - + +
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Residues in contact with GLY 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 GLN 3.1 18.6 + - - -
98A ALA* 1.4 74.4 - - - +
100A LEU* 1.4 62.6 + - - +
101A LYS* 3.3 22.2 + - - +
384A LYS* 3.3 34.3 + - - +
387A ALA* 4.9 2.3 - - - +
388A ILE* 4.2 10.5 - - - -
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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* 3.0 31.7 + - + +
97A LEU* 4.3 3.1 - - + +
99A GLY* 1.4 74.7 - - - +
101A LYS* 1.4 69.0 + - - +
102A VAL* 4.2 21.5 - - + +
380A TRP* 4.2 25.4 - - + -
384A LYS* 4.1 7.2 - - - +
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Residues in contact with LYS 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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97A LEU 3.4 4.0 + - - -
98A ALA 3.6 12.6 - - - +
99A GLY 3.3 17.0 + - - +
100A LEU* 1.4 79.3 - - - +
102A VAL* 1.4 64.0 + - - +
103A ILE 3.3 12.1 - - - -
104A LYS* 3.5 33.1 - - + +
383A ASP* 5.5 2.2 + - - -
387A ALA* 4.0 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
------------------------------------------------------------
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