Contacts of the strand formed by residues 97 - 104 (chain K) in PDB entry 5HJD
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 LYS 97 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86K GLU* 3.2 28.3 + - + +
87K VAL 3.2 15.5 - - - +
88K TYR* 3.4 41.7 + - + +
89K PHE* 3.7 7.0 - - - -
95K PRO* 3.3 17.8 - - - +
96K ARG* 1.3 84.1 - - + +
98K VAL* 1.3 66.3 + - - +
99K ARG* 6.0 2.9 - - + -
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Residues in contact with VAL 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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11K LEU* 4.9 0.2 - - + -
85K ILE 3.7 1.2 - - - +
86K GLU* 3.5 4.2 - - - +
87K VAL* 3.1 39.6 + - + -
89K PHE* 3.7 21.3 - - + -
97K LYS* 1.3 77.9 - - - +
99K ARG* 1.3 66.3 + - - +
100K PHE* 3.6 37.0 + - + -
122K LEU* 3.9 20.4 - - + -
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Residues in contact with ARG 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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54K HIS* 6.2 0.4 - - - -
84K PRO* 3.5 22.7 - - - +
85K ILE 3.5 9.9 - - - -
86K GLU* 4.1 25.0 + - + +
97K LYS* 6.0 3.8 - - - -
98K VAL* 1.3 81.0 - - - +
100K PHE* 1.3 74.4 + - - +
101K ASP* 2.4 45.0 + - - +
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Residues in contact with PHE 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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11K LEU* 4.6 10.1 - - + -
13K LEU* 3.7 33.7 - - + -
84K PRO* 3.2 1.7 - - - +
85K ILE* 2.6 45.4 + - + +
87K VAL* 4.4 12.3 - - + -
98K VAL* 3.6 39.7 - - + -
99K ARG* 1.3 77.7 - - - +
101K ASP* 1.3 62.2 + - - +
102K TYR* 3.4 4.5 + - + +
118K ARG* 3.7 25.4 - - - +
120K GLU* 3.7 31.0 - - + -
122K LEU* 3.9 17.7 - - + -
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Residues in contact with ASP 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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82K ILE* 4.1 20.3 - - + +
84K PRO* 3.3 19.0 - - - +
99K ARG* 2.4 36.5 + - - +
100K PHE* 1.3 69.8 - - - +
102K TYR* 1.3 63.1 + - - +
103K ASP* 3.6 2.8 + - - +
118K ARG* 3.7 14.3 + - - +
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Residues in contact with TYR 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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13K LEU* 3.8 25.1 - - + -
14K GLY* 3.1 24.2 - - - -
15K HIS* 2.5 57.3 + + + -
34K VAL* 4.2 12.8 - - + -
82K ILE* 3.6 1.8 - - - -
83K LEU* 2.6 51.1 + - + +
85K ILE* 3.8 16.4 - - + -
100K PHE* 3.4 3.2 + - + +
101K ASP* 1.3 72.1 - - - +
103K ASP* 1.3 75.4 + - - +
104K LEU* 3.3 10.5 + - + -
116K HIS* 3.7 12.5 + + - -
118K ARG* 4.0 24.9 - - + +
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Residues in contact with ASP 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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15K HIS* 4.0 0.2 - - - -
81K PHE 3.9 0.2 - - - +
82K ILE* 3.6 20.9 - - + +
101K ASP 3.6 3.9 + - - +
102K TYR* 1.3 84.5 - - - +
104K LEU* 1.3 58.6 + - - +
105K PHE* 3.2 34.7 + - + +
116K HIS* 6.0 0.2 - - - -
118K ARG* 4.7 3.0 - - - +
17M ARG* 2.2 37.8 + - - -
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Residues in contact with LEU 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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15K HIS* 3.8 24.9 - - + -
32K TRP* 3.6 37.7 - - + +
34K VAL* 3.7 31.2 - - + -
79K ALA 5.2 0.2 - - - +
80K GLY* 3.2 7.0 - - - -
81K PHE* 2.9 66.6 + - + +
83K LEU* 4.0 16.6 - - + -
102K TYR* 3.3 10.2 + - + -
103K ASP* 1.3 69.5 - - - +
105K PHE* 1.3 58.7 + - - +
106K LEU* 4.7 5.2 - - + -
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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