Contacts of the strand formed by residues 95 - 102 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26I VAL* 4.8 1.6 - - + -
27I GLN 2.9 11.2 + - - +
28I ALA* 3.4 6.8 - - + -
29I MET* 3.0 24.4 + - - -
50I GLU* 2.8 27.9 + - - +
51I PRO* 3.7 32.8 + - + -
57I LEU* 5.5 0.2 - - + -
84I MET* 4.1 30.1 - - + +
85I PHE 3.4 15.0 - - - +
86I ARG* 4.5 14.9 - - - +
87I ASP* 3.7 13.4 - - - +
92I ASP* 4.7 2.4 + - - -
93I PRO 3.3 16.1 + - - +
94I ASN* 1.3 83.6 + - - +
96I LEU* 1.3 60.8 + - - +
97I VAL* 4.6 6.7 - - + -
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Residues in contact with LEU 96 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29I MET* 3.7 21.3 - - + -
31I ILE* 3.8 14.6 - - + -
83I ALA 4.2 0.2 - - - +
84I MET* 3.4 4.3 - - - +
85I PHE* 2.8 41.6 + - + +
86I ARG 3.9 5.2 - - - +
87I ASP* 3.5 36.1 - - - +
88I PRO* 3.7 22.0 - - + -
89I PHE* 4.5 6.3 - - + -
95I LYS* 1.3 71.0 - - - +
97I VAL* 1.3 64.1 + - - +
98I LEU 4.2 0.9 - - - -
186I ALA* 5.0 0.7 - - + -
220I VAL* 4.4 11.7 - - + -
223I PHE* 4.3 13.9 - - + -
224I ILE* 4.0 25.1 - - + -
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Residues in contact with VAL 97 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28I ALA* 4.3 10.1 - - + -
29I MET 2.8 15.2 + - - +
30I TYR* 3.4 20.4 - - + -
31I ILE* 2.7 36.7 + - - +
54I VAL* 4.7 2.5 - - + -
57I LEU* 3.4 34.3 - - + -
81I PRO* 3.8 27.1 - - + -
82I ALA 4.7 0.2 - - - +
83I ALA 3.6 7.0 - - - +
84I MET* 4.7 0.2 - - + -
95I LYS* 4.6 4.7 - - + -
96I LEU* 1.3 80.7 - - - +
98I LEU* 1.3 62.6 + - - +
99I CYS* 3.6 6.0 + - - -
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Residues in contact with LEU 98 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31I ILE* 3.8 27.0 - - + +
32I TRP* 5.1 2.7 - - - -
33I ILE* 5.5 5.4 - - + -
40I LEU* 5.2 3.4 - - + -
81I PRO* 3.8 1.0 - - - +
82I ALA* 2.8 32.3 + - + +
83I ALA* 2.8 23.8 + - + +
85I PHE* 5.6 0.2 - - - -
96I LEU 4.2 0.8 - - - -
97I VAL* 1.3 69.3 - - - +
99I CYS* 1.3 64.5 + - - +
114I ARG* 4.8 5.2 - - - +
216I ASP* 3.5 45.8 - - - +
219I TRP* 4.2 23.1 - - + -
220I VAL* 3.9 19.1 - - + +
349I PHE* 4.5 10.5 - - + -
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Residues in contact with CYS 99 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30I TYR* 3.5 34.3 - - - -
31I ILE 2.9 19.3 + - - +
32I TRP* 4.3 8.9 - - - +
33I ILE* 5.1 1.9 + - - +
79I LEU* 4.0 19.3 - - + -
80I VAL 3.4 7.0 - - - +
81I PRO* 4.0 17.9 - - - -
82I ALA* 4.6 2.2 - - - -
97I VAL* 3.9 11.2 - - - -
98I LEU* 1.3 85.6 - - - +
100I GLU* 1.3 69.0 - - - +
101I VAL* 4.3 0.9 + - - +
114I ARG* 5.7 1.1 - - - -
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Residues in contact with GLU 100 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78I TYR 3.5 0.9 - - - +
79I LEU* 3.5 5.9 - - - -
80I VAL* 2.9 34.8 + - + +
82I ALA* 4.5 3.9 - - + +
99I CYS* 1.3 74.7 - - - +
101I VAL* 1.3 62.0 + - - +
102I PHE* 3.5 19.2 - - + -
112I ASN* 2.7 36.6 + - - +
114I ARG* 3.0 50.0 + - + +
115I HIS* 3.3 27.8 + - - +
118I LYS* 5.5 2.1 - - - +
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Residues in contact with VAL 101 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32I TRP* 3.6 40.8 - - + -
33I ILE* 3.9 11.7 - - + +
62I PHE* 3.7 24.5 - - + -
69I GLN* 4.3 4.5 - - - +
77I MET* 4.0 6.5 - - + -
78I TYR 3.4 3.6 - - - +
79I LEU* 4.1 4.0 - - + -
99I CYS 5.0 0.9 - - - +
100I GLU* 1.3 73.4 - - - +
102I PHE* 1.3 70.8 + - - +
109I ALA* 3.1 33.2 + - + -
111I THR* 6.0 0.7 - - - +
112I ASN* 3.1 24.5 + - + +
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Residues in contact with PHE 102 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77I MET* 3.5 12.1 - - - +
78I TYR* 2.9 40.0 + - + -
80I VAL* 3.5 35.9 - - + -
100I GLU* 3.5 38.1 - - + -
101I VAL* 1.3 73.5 - - - +
103I LYS* 1.3 64.2 + - - +
106I ARG* 3.6 28.9 - - - +
107I ARG 3.2 8.7 - - - +
108I PRO* 3.6 25.4 - - + -
109I ALA 4.2 0.7 - - - +
112I ASN* 4.0 6.3 - - - -
115I HIS* 3.8 26.5 - + - -
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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