Contacts of the strand formed by residues 95 - 102 (chain H) in PDB entry 2QC8
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 95 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26H VAL* 4.9 0.9 - - + -
27H GLN 2.9 14.1 + - - +
28H ALA* 3.4 5.7 - - + -
29H MET* 2.8 33.3 + - - +
50H GLU* 2.8 28.3 + - - -
51H PRO* 3.4 37.7 + - + -
57H LEU* 5.4 0.2 - - + -
84H MET* 4.0 29.6 - - + -
85H PHE 3.3 14.1 - - - +
86H ARG* 4.6 7.6 - - + +
87H ASP* 4.1 6.3 - - - +
92H ASP* 4.0 12.9 + - - -
93H PRO 3.5 14.4 + - - +
94H ASN* 1.3 78.8 - - - +
96H LEU* 1.3 60.3 + - - +
97H VAL* 4.6 6.3 - - + -
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Residues in contact with LEU 96 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29H MET* 3.6 21.3 - - + -
31H ILE* 3.9 19.1 - - + -
83H ALA 3.9 0.5 - - - +
84H MET* 3.4 2.9 - - - +
85H PHE* 2.7 49.8 + - + +
86H ARG 4.0 4.3 - - - +
87H ASP* 3.7 31.8 - - - +
88H PRO* 3.8 21.5 - - + -
89H PHE* 4.4 7.0 - - + -
95H LYS* 1.3 72.8 - - - +
97H VAL* 1.3 59.7 + - - +
98H LEU 4.3 0.2 - - - -
220H VAL* 4.2 13.9 - - + -
223H PHE* 4.2 11.7 - - + -
224H ILE* 4.0 22.4 - - + -
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Residues in contact with VAL 97 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28H ALA* 4.6 7.2 - - + -
29H MET 2.9 11.5 + - - +
30H TYR* 3.4 18.1 - - + -
31H ILE* 2.7 36.5 + - - +
54H VAL* 4.5 2.0 - - + -
57H LEU* 3.0 42.8 - - + -
81H PRO* 3.8 22.7 - - + -
82H ALA 4.4 0.4 - - - +
83H ALA 3.4 7.2 - - - +
84H MET* 4.6 0.9 - - + -
95H LYS* 4.6 4.7 - - + -
96H LEU* 1.3 79.0 - - - +
98H LEU* 1.3 68.0 + - - +
99H CYS* 3.8 5.2 + - - -
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Residues in contact with LEU 98 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31H ILE* 3.7 25.8 - - + +
32H TRP* 5.2 2.0 - - - -
33H ILE* 5.2 5.8 - - + -
40H LEU* 5.0 5.2 - - + -
82H ALA* 2.7 32.6 + - + +
83H ALA* 2.7 21.4 + - + +
96H LEU 4.3 0.4 - - - -
97H VAL* 1.3 74.2 - - - +
99H CYS* 1.3 64.0 + - - +
114H ARG* 5.1 3.6 - - - +
216H ASP* 3.4 50.0 - - + +
219H TRP* 4.2 22.4 - - + -
220H VAL* 3.9 18.3 - - + +
349H PHE* 4.6 7.6 - - + -
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Residues in contact with CYS 99 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30H TYR* 3.7 31.9 - - - -
31H ILE 2.9 21.6 + - - +
32H TRP* 4.5 6.9 - - - +
33H ILE* 5.1 6.1 + - - +
79H LEU* 3.8 24.5 - - + -
80H VAL 3.4 11.4 - - - +
81H PRO* 3.9 17.3 - - - -
82H ALA* 4.2 3.4 - - - +
97H VAL* 4.0 7.9 - - - -
98H LEU* 1.3 88.4 - - - +
100H GLU* 1.3 63.2 + - - +
101H VAL* 4.3 1.0 + - - +
114H ARG* 5.4 1.4 - - - -
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Residues in contact with GLU 100 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78H TYR 3.7 3.3 - - - +
79H LEU* 3.7 1.7 - - - -
80H VAL* 3.1 32.8 + - + +
82H ALA* 4.4 3.5 - - + +
99H CYS* 1.3 74.8 - - - +
101H VAL* 1.3 62.9 + - - +
102H PHE* 3.3 17.6 - - + -
112H ASN* 2.9 31.5 + - - +
114H ARG* 3.0 52.2 + - + +
115H HIS* 3.1 30.1 + - - +
118H LYS* 5.4 2.6 - - - +
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Residues in contact with VAL 101 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32H TRP* 3.8 38.4 - - + -
33H ILE* 4.0 11.7 - - + +
62H PHE* 3.8 20.9 - - + -
69H GLN* 4.4 3.6 - - - +
77H MET* 3.5 28.3 - - + -
78H TYR 3.5 3.8 - - - +
79H LEU* 4.3 1.6 - - + -
99H CYS 5.1 0.4 - - - +
100H GLU* 1.3 76.6 - - - +
102H PHE* 1.3 64.6 + - - +
109H ALA* 3.0 30.2 + - + -
111H THR* 6.0 0.4 - - - +
112H ASN* 3.1 21.7 + - + +
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Residues in contact with PHE 102 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77H MET* 3.4 13.0 - - - +
78H TYR* 3.0 41.1 + - + -
80H VAL* 4.0 28.5 - - + -
100H GLU* 3.3 46.7 - - + -
101H VAL* 1.3 76.1 - - - +
103H LYS* 1.3 62.6 + - - +
106H ARG* 3.6 25.4 - - - +
107H ARG 3.2 4.9 - - - +
108H PRO* 3.6 29.4 - - + -
109H ALA 4.0 0.2 - - - +
112H ASN* 3.9 0.7 - - - -
115H HIS* 3.7 24.7 - + - -
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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