Contacts of the strand formed by residues 43 - 51 (chain C) in PDB entry 4QUL
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 GLU 43 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41C TYR* 3.8 3.5 - - - +
42C PRO* 1.3 87.7 - - + +
44C MET* 1.3 59.8 + - - +
45C GLY* 4.1 4.5 - - - +
84C GLU* 3.9 18.4 - - - +
110C LYS* 3.0 33.0 + - - +
111C ARG* 3.2 30.6 + - + +
112C SER* 2.8 30.2 + - - -
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Residues in contact with MET 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C MET* 3.6 35.4 - - + +
43C GLU* 1.3 72.3 - - - +
45C GLY* 1.3 56.9 + - - +
81C LEU 3.5 24.2 - - - +
82C LYS* 3.5 29.3 + - + +
83C TYR* 4.0 12.8 - - + -
112C SER* 3.2 2.7 + - - -
113C SER* 2.8 37.3 + - - -
275C PHE* 3.8 39.3 - - + +
277C HIS* 3.8 24.7 - - + +
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Residues in contact with GLY 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C GLU* 3.2 6.2 - - - +
44C MET* 1.3 80.5 - - - +
46C LEU* 1.3 64.3 + - - -
82C LYS 4.7 0.8 + - - -
83C TYR* 3.3 9.3 - - - -
84C GLU* 3.0 26.7 + - - +
111C ARG* 3.6 19.5 - - - -
113C SER 3.4 11.4 - - - -
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Residues in contact with LEU 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C GLY* 1.3 74.4 - - - -
47C CYS* 1.3 60.9 + - - +
48C ILE* 4.3 7.2 - - + -
83C TYR* 3.8 2.7 - - - -
84C GLU* 3.6 32.8 - - - +
86C ARG* 3.3 38.8 - - - +
103C VAL* 3.9 23.1 - - + -
106C GLU* 3.6 20.6 - - - +
108C HIS* 3.9 3.6 + - + -
111C ARG* 3.7 22.6 - - - +
113C SER 4.0 3.6 + - - -
114C PHE* 3.9 14.2 - - + -
115C VAL* 3.0 26.9 + - - +
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Residues in contact with CYS 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C GLY 3.9 0.2 + - - -
46C LEU* 1.3 73.9 - - - +
48C ILE* 1.3 61.1 + - - +
49C ILE* 3.7 22.1 + - - -
78C PHE* 3.7 33.0 - - + -
83C TYR* 3.8 21.1 - - + -
84C GLU 3.0 9.7 + - - +
85C VAL* 3.4 6.2 - - - +
86C ARG 2.9 26.6 + - - +
115C VAL* 3.2 22.9 - - + -
117C VAL* 4.3 4.0 - - - -
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Residues in contact with ILE 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C LEU* 4.3 10.1 - - + -
47C CYS* 1.3 73.9 - - - +
49C ILE* 1.3 58.8 + - - +
50C ILE* 4.0 9.4 + - + -
86C ARG* 3.6 36.6 - - + +
88C LYS* 4.8 5.6 - - + +
99C LEU* 4.1 15.0 - - + -
100C MET* 3.7 24.7 - - + -
103C VAL* 4.0 21.8 - - + -
114C PHE* 3.8 26.5 - - + -
115C VAL 2.8 12.5 + - - +
116C CYS* 3.4 5.3 - - + -
117C VAL* 2.7 33.4 + - - +
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Residues in contact with ILE 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C CYS* 4.0 16.4 - - - -
48C ILE* 1.3 77.9 - - - +
50C ILE* 1.3 65.3 + - - +
51C ASN 4.7 0.9 - - - +
71C ALA* 4.1 3.1 - - + +
74C LEU* 3.7 29.4 - - + -
75C ARG 4.0 6.3 - - - +
85C VAL* 3.7 25.6 - - + -
86C ARG 2.9 10.4 + - - +
87C ASN* 3.7 25.6 - - - +
88C LYS* 2.8 31.2 + - - +
117C VAL* 3.5 15.3 - - + +
119C LEU* 4.1 25.6 - - + -
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Residues in contact with ILE 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C ILE* 4.1 6.1 - - + +
49C ILE* 1.3 77.9 - - - +
51C ASN* 1.3 58.7 + - - +
52C ASN* 4.1 21.3 - - - +
88C LYS* 3.5 2.9 - - + -
91C LEU* 4.2 18.2 - - + -
96C ILE* 4.2 26.0 - - + -
99C LEU* 3.9 29.6 - - + -
100C MET* 4.2 14.4 - - + -
116C CYS* 4.8 1.1 - - - -
117C VAL 2.8 13.9 + - - +
118C LEU* 3.7 26.2 - - + -
119C LEU* 2.9 31.8 + - - +
120C SER* 6.4 0.9 - - - -
127C ILE* 6.4 0.2 - - + -
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Residues in contact with ASN 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C ILE* 4.8 3.4 - - + -
50C ILE* 1.3 72.7 - - - +
52C ASN* 1.3 59.9 + - - +
53C LYS* 3.7 3.3 + - - +
67C THR* 2.7 36.5 + - - +
68C ASP* 2.9 28.5 + - - +
71C ALA* 3.8 25.9 - - + +
87C ASN* 5.0 2.2 - - - +
88C LYS 2.7 11.8 + - - +
89C ASN* 3.1 28.8 + - - +
90C ASP* 2.9 20.3 + - - +
119C LEU* 3.6 8.0 - - + +
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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