Contacts of the helix formed by residues 85 - 102 (chain I) in PDB entry 2WWB
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 ALA 85 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51I VAL* 5.7 1.8 - - + +
52I LEU* 4.1 28.2 - - + +
83I TRP* 3.5 6.3 + - + +
84I PRO* 1.4 70.4 - - - +
86I LYS* 1.4 61.0 + - - +
87I SER 3.4 0.7 - - - -
88I VAL* 3.3 14.2 + - + +
89I LYS* 3.2 22.9 + - - +
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Residues in contact with LYS 86 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1666F C 3.8 11.0 - - - +
1667F A 3.0 44.7 + - - -
23I ARG 3.2 24.2 + - - -
24I VAL* 3.3 30.5 - - + +
25I SER* 5.5 3.8 - - - +
84I PRO* 4.7 7.0 - - + -
85I ALA* 1.4 79.4 - - - +
87I SER* 1.4 60.8 + - - +
89I LYS* 3.6 15.7 + - - +
90I PHE 3.6 5.5 + - - -
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Residues in contact with SER 87 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24I VAL* 3.5 14.4 - - - +
25I SER* 4.2 4.2 - - - -
28I ASN* 3.4 24.4 - - - +
29I THR* 3.1 22.3 + - - -
32I THR* 4.2 18.6 - - - +
84I PRO* 3.5 11.3 + - - +
85I ALA 3.4 0.2 - - - -
86I LYS* 1.4 74.5 - - - +
88I VAL* 1.3 64.1 + - - +
89I LYS 3.4 0.2 - - - -
90I PHE* 3.6 2.1 - - - +
91I VAL* 3.2 28.6 + - - +
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Residues in contact with VAL 88 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32I THR* 5.7 4.3 - - + +
48I LEU* 3.4 48.6 - - + +
51I VAL* 3.6 24.0 - - + -
52I LEU* 5.2 8.7 - - + +
57I ALA* 5.2 5.2 - - + -
58I ILE* 6.4 1.8 - - + -
84I PRO 3.4 18.4 - - - +
85I ALA* 3.5 13.7 - - + +
86I LYS 3.3 0.6 - - - -
87I SER* 1.3 77.2 - - - +
89I LYS* 1.4 59.2 + - - +
91I VAL* 3.4 3.6 + - - +
92I GLN* 3.0 33.5 + - + +
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Residues in contact with LYS 89 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542E A 5.3 11.2 - - - +
1667F A 4.3 1.8 + - - -
1668F G 3.1 36.8 + - - -
24I VAL* 6.3 0.4 - - + -
85I ALA 3.2 12.0 + - - +
86I LYS* 3.8 13.7 - - + +
87I SER 3.4 0.4 - - - -
88I VAL* 1.4 75.8 - - - +
90I PHE* 1.4 58.0 + - - +
92I GLN* 3.7 6.6 + - - +
93I GLY* 3.2 19.1 + - - -
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Residues in contact with PHE 90 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19I GLY* 4.6 2.7 - - - -
22I LEU* 3.7 34.9 - - + +
24I VAL* 3.5 47.5 - - + +
29I THR* 3.5 37.7 - - + -
86I LYS 3.6 2.4 + - - +
87I SER 3.6 8.3 - - - +
89I LYS* 1.4 77.7 - - - +
91I VAL* 1.4 57.6 + - + +
93I GLY* 3.3 3.7 + - - -
94I LEU* 3.1 23.3 + - + +
144I SER* 3.4 26.2 - - - -
145I HIS* 4.6 0.4 - - - -
146I ILE* 3.4 34.3 - - + -
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Residues in contact with VAL 91 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29I THR* 4.2 21.8 - - + -
32I THR* 3.8 18.6 - - + -
33I ALA* 5.5 0.9 - - - +
36I ILE* 4.2 24.2 - - + -
48I LEU* 3.6 23.6 - - + -
87I SER 3.2 18.7 + - - +
88I VAL 3.4 0.6 + - - +
90I PHE* 1.4 74.9 - - + +
92I GLN* 1.4 59.4 + - - +
94I LEU* 3.3 12.4 + - + +
95I LEU* 2.9 34.5 + - + +
117I ILE* 5.4 3.1 - - + -
146I ILE* 5.1 7.0 - - + -
148I LEU* 6.4 0.4 - - + -
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Residues in contact with GLN 92 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45I GLN* 3.7 14.4 - - - +
48I LEU* 3.5 35.3 - - + +
49I GLU* 3.4 33.4 + - - +
88I VAL* 3.0 25.5 + - + +
89I LYS* 3.9 7.9 - - - +
90I PHE 3.4 0.2 - - - -
91I VAL* 1.4 76.0 - - - +
93I GLY* 1.4 55.1 + - - +
95I LEU* 3.5 14.3 + - - +
96I GLN* 3.1 36.0 + - - +
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Residues in contact with GLY 93 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89I LYS 3.2 15.0 + - - -
90I PHE 3.3 4.2 + - - -
91I VAL 3.3 0.2 - - - -
92I GLN* 1.4 73.7 - - - +
94I LEU* 1.4 62.0 + - - +
96I GLN* 3.5 25.3 - - - +
97I ASN* 3.6 12.3 + - - +
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Residues in contact with LEU 94 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17I ALA* 3.6 29.4 - - + -
18I ARG* 3.9 11.2 - - - +
19I GLY* 4.4 3.1 - - - +
90I PHE* 3.1 14.0 + - + +
91I VAL* 3.4 16.2 - - + +
93I GLY* 1.4 77.4 - - - +
95I LEU* 1.4 57.1 + - - +
97I ASN* 3.6 4.6 + - + +
98I ALA* 3.0 25.1 + - - +
117I ILE* 4.3 7.2 - - + -
146I ILE* 3.5 45.5 - - + -
147I GLU 4.9 0.4 - - - -
148I LEU* 3.7 32.5 - - + -
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Residues in contact with LEU 95 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36I ILE* 5.1 8.3 - - + -
41I LEU* 4.0 30.6 - - + +
44I ALA* 3.9 31.2 - - + -
45I GLN* 4.2 6.5 - - + +
48I LEU* 3.8 15.9 - - + -
91I VAL* 2.9 25.8 + - + +
92I GLN* 3.6 25.8 - - - +
93I GLY 3.4 0.2 - - - -
94I LEU* 1.4 75.4 - - + +
96I GLN* 1.4 59.0 + - - +
98I ALA* 3.4 3.9 + - - +
99I ALA* 2.9 30.5 + - - +
114I VAL* 5.4 2.2 - - + -
148I LEU* 4.2 15.7 - - + -
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Residues in contact with GLN 96 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541E G 4.1 31.9 + - - +
542E A 4.4 6.3 + - - -
543E A 6.0 1.6 - - - +
92I GLN* 3.1 22.7 + - - +
93I GLY* 3.5 20.3 - - - +
95I LEU* 1.4 72.4 - - - +
97I ASN* 1.4 62.4 + - + +
99I ALA* 3.6 6.5 + - - +
100I ALA* 3.1 27.7 + - - +
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Residues in contact with ASN 97 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540E U 4.1 22.3 + - - -
541E G 4.7 8.2 + - - +
544E A 5.3 2.4 - - - +
545E A 4.2 10.3 - - - -
546E G 3.4 19.8 + - - +
17I ALA* 3.4 20.9 - - + +
18I ARG 4.3 4.6 + - - +
93I GLY 3.6 13.7 + - - +
94I LEU* 3.6 6.1 + - + +
95I LEU 3.4 0.4 - - - -
96I GLN* 1.4 79.6 - - + +
98I ALA* 1.4 58.1 + - - +
100I ALA* 3.3 4.0 + - - +
101I ASN* 3.0 53.6 + - - +
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Residues in contact with ALA 98 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I ALA* 4.3 4.6 - - - +
16I SER 4.4 5.8 - - - +
17I ALA* 3.8 15.0 - - + +
41I LEU* 4.5 11.3 - - + +
94I LEU 3.0 18.8 + - - +
95I LEU* 3.6 6.7 - - - +
96I GLN 3.4 0.2 - - - -
97I ASN* 1.4 76.3 - - - +
99I ALA* 1.4 55.0 + - - +
101I ASN* 3.7 2.6 + - - +
102I ALA* 3.0 27.8 + - - +
148I LEU* 3.8 23.3 - - + -
150I VAL* 5.5 6.8 - - + +
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Residues in contact with ALA 99 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41I LEU* 3.8 25.8 - - + -
95I LEU 2.9 18.4 + - - +
96I GLN* 4.0 7.0 - - - +
98I ALA* 1.4 75.1 - - - +
100I ALA* 1.4 57.1 + - - +
102I ALA* 3.2 23.2 - - - +
103I GLU* 3.3 8.3 + - - +
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Residues in contact with ALA 100 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540E U 3.2 46.7 - - - +
541E G 5.1 4.0 - - - +
96I GLN 3.1 17.9 + - - +
97I ASN* 3.7 2.5 - - - +
98I ALA 3.3 0.2 - - - -
99I ALA* 1.4 76.1 - - - +
101I ASN* 1.4 62.3 + - - +
102I ALA 3.2 1.1 - - - -
103I GLU* 3.2 15.8 + - - +
104I ALA* 3.6 11.8 + - - +
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Residues in contact with ASN 101 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540E U 4.6 2.9 + - - -
546E G 3.0 48.5 + - - -
547E A 3.6 16.0 + - - +
15I ALA* 4.5 7.9 - - + +
16I SER 2.9 29.4 + - - +
97I ASN* 3.0 33.5 + - - +
98I ALA 3.8 2.5 - - - +
100I ALA* 1.4 76.7 - - - +
102I ALA* 1.4 56.3 + - - +
103I GLU 3.2 3.5 + - - -
104I ALA* 3.7 12.8 + - - +
105I LYS* 3.9 10.7 + - - +
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Residues in contact with ALA 102 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I ALA* 3.7 19.7 - - + +
41I LEU* 4.5 11.2 - - + +
98I ALA 3.0 20.0 + - - +
99I ALA* 3.2 14.8 - - - +
100I ALA 3.2 0.2 - - - -
101I ASN* 1.4 73.1 - - - +
103I GLU* 1.4 58.4 + - - +
105I LYS* 3.5 26.6 - - + +
112I LEU* 6.0 4.0 - - + -
150I VAL* 5.3 3.4 - - + -
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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
------------------------------------------------------------
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