Contacts of the helix formed by residues 91 - 104 (chain K) 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 ASN 91 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60K TYR* 3.8 5.3 + - - +
62K VAL* 4.7 2.0 - - - +
89K LYS 4.7 1.6 - - - +
90K ALA* 1.4 74.9 - - - +
92K LYS* 1.4 74.7 + - - +
93K TYR* 3.4 19.3 - - - +
94K GLN* 3.4 28.8 + - - +
95K ILE* 3.3 22.2 + - - +
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Residues in contact with LYS 92 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91K ASN* 1.4 80.7 + - - +
93K TYR* 1.4 62.9 + - - +
95K ILE* 3.5 5.3 + - - +
96K LYS* 3.3 20.8 + - - +
110K VAL* 4.0 37.1 + - + +
111K ASN* 3.6 8.3 - - - +
112K THR* 3.2 45.9 + - + +
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Residues in contact with TYR 93 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91K ASN* 3.4 15.1 - - - +
92K LYS* 1.4 78.8 - - - +
94K GLN* 1.4 69.3 + - + +
96K LYS* 3.4 19.7 + - + +
97K LYS* 3.1 55.9 + - + +
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Residues in contact with GLN 94 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59K SER* 4.0 17.4 + - - -
60K TYR* 3.0 53.7 + - - -
62K VAL* 3.5 20.9 - - + +
91K ASN* 3.4 18.8 + - + +
92K LYS 3.4 0.6 - - - -
93K TYR* 1.4 85.1 - - + +
95K ILE* 1.4 59.6 + - - +
97K LYS* 3.9 9.1 - - + +
98K ALA* 3.1 28.6 + - - +
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Residues in contact with ILE 95 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62K VAL* 4.5 8.3 - - + -
63K ILE* 5.6 1.8 - - + -
84K PHE* 5.4 1.3 - - + -
86K VAL* 4.0 33.7 - - + -
90K ALA* 4.5 3.4 - - + -
91K ASN 3.3 20.4 + - - +
92K LYS 3.7 5.4 - - - +
93K TYR 3.3 0.4 - - - -
94K GLN* 1.4 74.4 - - - +
96K LYS* 1.4 62.8 + - - +
98K ALA* 3.5 4.1 + - - +
99K VAL* 3.3 30.5 + - + +
107K VAL* 5.1 0.7 - - - +
110K VAL* 4.0 13.7 - - + -
112K THR* 3.7 30.1 - - + -
122K ALA* 4.1 7.2 - - + -
124K VAL* 3.8 29.4 - - + -
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Residues in contact with LYS 96 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92K LYS 3.3 11.2 + - - +
93K TYR* 3.4 26.0 - - + +
95K ILE* 1.4 78.8 - - - +
97K LYS* 1.4 62.4 + - - +
99K VAL 3.9 0.2 + - - -
100K LYS* 3.5 24.7 + - + +
106K ASP* 3.5 18.9 + - - +
107K VAL* 3.0 55.1 + - + +
110K VAL* 4.4 11.4 - - + +
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Residues in contact with LYS 97 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93K TYR* 3.1 43.4 + - + +
94K GLN* 3.9 9.4 - - + +
95K ILE 3.3 0.2 - - - -
96K LYS* 1.4 77.3 - - + +
98K ALA* 1.4 64.0 + - - +
100K LYS* 3.3 20.0 - - + +
101K GLU* 3.1 42.6 + - + +
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Residues in contact with ALA 98 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61K LYS 5.2 1.3 - - - +
62K VAL* 3.6 20.4 - - + -
63K ILE* 3.9 15.5 - - + -
94K GLN 3.1 19.7 + - - +
95K ILE 3.9 4.3 - - - +
96K LYS 3.5 0.2 - - - -
97K LYS* 1.4 75.9 - - - +
99K VAL* 1.4 60.0 + - - +
101K GLU* 3.3 5.5 + - - +
102K LEU* 3.2 36.1 + - + +
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Residues in contact with VAL 99 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63K ILE* 3.8 17.0 - - + -
82K LEU* 5.3 0.9 - - + -
84K PHE* 3.8 32.1 - - + -
95K ILE* 3.3 20.0 + - + +
96K LYS 4.5 2.0 - - - +
98K ALA* 1.4 72.7 - - - +
100K LYS* 1.4 62.6 + - - +
101K GLU 3.3 0.2 - - - -
102K LEU 4.0 0.2 - - - -
103K TYR* 3.2 41.7 + - + +
104K GLU 3.6 1.9 + - - -
105K VAL* 3.6 21.9 - - + +
107K VAL* 4.6 3.8 - - + -
124K VAL* 4.7 7.9 - - + -
126K LEU* 3.9 16.6 - - + -
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Residues in contact with LYS 100 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96K LYS* 3.5 19.7 + - + +
97K LYS* 3.3 15.0 + - + +
99K VAL* 1.4 78.8 - - - +
101K GLU* 1.4 70.4 + - + +
102K LEU 3.4 0.2 - - - -
104K GLU* 3.1 58.6 + - - +
105K VAL* 3.4 31.1 - - + +
106K ASP* 5.6 0.4 - - - -
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Residues in contact with GLU 101 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97K LYS* 3.1 48.6 + - + +
98K ALA* 3.3 7.2 + - - +
100K LYS* 1.4 91.9 - - + +
102K LEU* 1.4 67.9 + - + +
104K GLU 5.0 0.2 - - - -
26N LYS* 5.6 4.2 - - - -
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Residues in contact with LEU 102 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63K ILE* 4.3 20.0 - - + -
98K ALA* 3.2 25.6 + - + +
100K LYS 3.4 0.2 - - - -
101K GLU* 1.4 85.8 - - + +
103K TYR* 1.4 72.3 + - + +
138K ARG* 3.1 29.2 + - - +
26N LYS* 5.1 20.0 - - + -
29N ALA* 5.4 13.7 - - + -
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Residues in contact with TYR 103 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63K ILE* 5.1 0.4 - - + -
66K PRO* 4.7 5.7 - - - +
82K LEU* 4.2 4.5 - - + -
84K PHE* 3.7 32.1 - + - -
99K VAL* 3.2 27.7 + - + +
101K GLU 3.8 0.2 - - - -
102K LEU* 1.4 104.9 - - + +
104K GLU* 1.4 74.5 + - - +
105K VAL* 3.6 6.1 - - + -
130K TYR* 3.4 28.4 - - - +
135K ILE* 3.5 32.5 - - + +
138K ARG* 3.3 27.5 + - - +
139K ILE* 3.7 37.4 - - + +
29N ALA 5.0 4.3 + - - -
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Residues in contact with GLU 104 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99K VAL 3.6 0.6 + - - -
100K LYS* 3.1 47.8 + - - +
101K GLU 5.0 0.2 - - - -
103K TYR* 1.4 83.5 - - - +
105K VAL* 1.4 61.2 + - - +
130K TYR* 4.1 7.6 - - - -
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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