Contacts of the strand formed by residues 98 - 101 (chain K) in PDB entry 3Q2K
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 HIS 98 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74K ASP* 3.0 21.1 + - + -
75K ALA* 3.3 14.1 - - + -
76K LEU 3.1 22.7 + - - -
92K VAL* 3.8 6.1 - - - +
96K GLY 5.4 1.1 + - - -
97K ARG* 1.3 76.5 - - - +
99K VAL* 1.3 61.1 + - - +
123K GLY 4.9 2.9 - - - -
124K VAL* 3.4 17.1 - - + +
125K ARG* 2.5 54.3 + - + +
127K PHE* 5.0 2.0 - - + -
312K LEU* 3.8 23.7 - - + +
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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
----------------------------------------------------------
76K LEU 3.8 3.6 - - - +
78K LEU* 3.7 27.8 - - + -
89K ALA* 3.7 34.1 - - + +
92K VAL* 3.7 18.2 - - + -
93K ALA 4.6 1.1 - - - +
97K ARG 4.6 2.2 - - - +
98K HIS* 1.3 76.9 - - - +
100K VAL* 1.3 64.4 + - - +
101K SER* 3.8 8.3 - - - +
119K CYS* 4.4 9.2 - - - -
125K ARG 2.9 9.7 + - - +
126K LEU* 3.3 27.5 - - + -
127K PHE* 2.8 27.6 + - - -
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Residues in contact with VAL 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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13K PHE* 4.7 11.9 - - + -
75K ALA* 5.1 4.5 - - + -
76K LEU 3.1 11.0 + - - +
77K VAL* 3.3 18.9 - - + +
78K LEU 2.8 24.4 + - - -
98K HIS 4.3 0.2 - - - -
99K VAL* 1.3 74.5 - - - +
101K SER* 1.3 58.1 + - - +
127K PHE* 3.5 36.3 - - + -
129K VAL* 4.0 22.9 - - + -
304K TYR* 4.4 7.6 - - + -
305K TYR* 4.8 8.1 - - + +
308K VAL* 3.8 20.9 - - + -
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Residues in contact with SER 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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78K LEU* 3.9 11.4 - - - -
85K HIS* 3.0 22.0 + - - +
99K VAL* 3.8 14.1 - - - +
100K VAL* 1.3 71.9 - - - +
102K GLU* 1.3 78.5 + - - +
105K MET* 3.9 6.8 - - - -
115K MET* 4.2 14.4 - - - -
126K LEU* 4.4 2.0 - - - -
127K PHE 2.8 14.5 + - - -
128K VAL* 3.3 6.9 - - - -
129K VAL* 2.9 29.3 + - - +
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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