Contacts of the strand formed by residues 97 - 107 (chain K) in PDB entry 6R90
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 SER 97 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92K LYS 4.2 0.5 - - - +
93K GLN* 3.5 1.2 - - - +
94K SER* 2.5 56.0 + - - -
96K GLU* 1.3 76.6 - - - +
98K ILE* 1.3 61.6 + - - +
99K ASP* 4.2 0.8 + - - -
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Residues in contact with ILE 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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52K VAL* 4.1 22.4 - - + +
53K LYS* 4.4 31.7 + - + -
91K TYR* 3.0 51.1 - - + +
92K LYS 3.5 6.1 - - - +
93K GLN* 3.5 32.1 - - + +
96K GLU* 3.6 14.7 + - - +
97K SER* 1.3 72.6 - - - +
99K ASP* 1.3 69.4 + - - +
100K ILE* 4.7 3.6 - - + -
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Residues in contact with ASP 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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92K LYS* 2.8 38.7 + - + +
97K SER* 4.2 1.3 - - - -
98K ILE* 1.3 74.5 - - - +
100K ILE* 1.3 88.8 + - - +
101K ILE* 3.5 19.4 - - + +
1063K LYS* 5.6 10.2 + - - +
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Residues in contact with ILE 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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23K PHE* 4.2 11.2 - - + -
41K ILE* 6.4 3.1 - - + -
53K LYS* 6.1 3.8 - - + -
55K VAL* 5.3 15.3 - - + -
89K LEU* 3.6 41.7 - - + +
90K GLU 3.5 11.7 - - - +
91K TYR* 3.5 45.3 - - + -
98K ILE* 4.7 3.1 - - + -
99K ASP* 1.3 86.9 + - - +
101K ILE* 1.3 59.4 + - - +
102K THR* 4.0 2.9 + - - -
1065K VAL* 4.7 19.4 - - + +
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Residues in contact with ILE 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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89K LEU* 3.8 4.6 - - - +
90K GLU* 3.2 34.8 + - + +
92K LYS* 4.0 28.9 - - + -
99K ASP* 3.5 26.2 - - + +
100K ILE* 1.3 75.2 - - - +
102K THR* 1.3 71.8 + - - +
103K ARG* 3.4 11.7 + - + +
1063K LYS* 6.2 2.0 - - - +
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Residues in contact with THR 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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88K ILE 4.4 2.7 - - - +
89K LEU* 4.2 4.5 - - + +
100K ILE 4.0 2.3 + - - -
101K ILE* 1.3 79.7 - - - +
103K ARG* 1.3 62.6 + - - +
104K ALA 3.9 24.5 - - - +
105K HIS* 4.1 7.0 - - + +
1064K SER 4.2 2.9 + - - -
1065K VAL* 4.3 1.9 - - - -
1066K GLY* 3.3 25.0 + - - -
1067K LYS* 3.7 47.9 + - + +
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Residues in contact with ARG 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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72K GLU* 3.3 31.9 + - - -
76K LEU* 4.1 16.2 - - + +
88K ILE* 3.2 21.3 + - + +
89K LEU 4.8 0.7 - - - -
90K GLU* 2.6 60.0 + - + +
101K ILE* 3.4 9.5 + - + +
102K THR* 1.3 74.6 - - - +
104K ALA* 1.3 62.4 + - + +
150K LYS* 3.9 25.7 + - - +
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Residues in contact with ALA 104 (chain K).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87K CYS* 3.3 5.0 - - - +
88K ILE* 2.9 43.5 + - + +
102K THR* 3.5 7.7 - - - +
103K ARG* 1.3 80.1 - - + +
105K HIS* 1.3 64.0 + - - +
149K ASN 4.0 1.8 - - - +
150K LYS* 3.5 17.9 - - - +
152K LEU* 3.7 25.1 - - + -
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Residues in contact with HIS 105 (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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86K ALA 3.4 11.2 - - - +
102K THR* 4.1 4.1 - - + +
104K ALA* 1.3 75.8 - - - +
106K GLY* 1.3 63.7 + - - +
150K LYS 2.9 22.4 + - - +
151K GLU* 3.3 10.6 - - + -
152K LEU* 3.6 7.0 - - - -
1066K GLY* 3.0 32.5 - - - +
1067K LYS* 3.4 45.5 + - + +
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Residues in contact with GLY 106 (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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85K ASN* 3.8 3.3 - - - -
86K ALA* 2.9 37.6 + - - +
105K HIS* 1.3 83.4 - - - +
107K ASN* 1.3 61.5 + - - -
108K VAL* 3.9 2.9 - - - -
151K GLU* 3.4 17.3 - - - -
152K LEU* 3.6 2.6 - - - +
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Residues in contact with ASN 107 (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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83K LYS 4.0 5.5 + - - -
84K TYR 3.7 4.9 - - - -
85K ASN* 3.5 25.2 - - - +
106K GLY* 1.3 70.0 - - - -
108K VAL* 1.3 60.6 + - - +
109K GLN* 2.9 43.7 + - - +
151K GLU 4.8 1.0 + - - -
152K LEU 5.9 0.2 - - - -
1072K PHE* 3.8 20.6 - - - -
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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