Contacts of the strand formed by residues 111 - 119 (chain C) in PDB entry 4QUG
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 ARG 111 (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* 3.9 3.7 - - - -
43C GLU* 3.2 30.9 + - + +
45C GLY* 3.7 26.2 - - - -
46C LEU* 3.7 23.1 - - - +
84C GLU* 4.3 6.3 + - - -
86C ARG* 4.1 4.2 - - - +
106C GLU* 3.1 29.7 + - - +
107C ASP 3.7 17.1 + - - -
108C HIS* 2.9 51.1 + - + +
110C LYS* 1.3 80.5 - - + +
112C SER* 1.3 63.5 + - - +
113C SER 3.4 5.2 - - - +
151C LEU* 5.0 0.4 - - + +
154C LYS* 2.9 27.9 + - - +
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Residues in contact with SER 112 (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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38C LYS 3.9 3.8 - - - +
39C MET* 3.2 53.6 + - - +
41C TYR* 3.2 24.3 + - - +
43C GLU 2.8 12.7 + - - -
44C MET* 3.3 11.6 + - - -
111C ARG* 1.3 72.6 - - - +
113C SER* 1.3 61.3 + - - +
154C LYS* 3.5 11.4 - - - +
155C PRO* 3.5 17.8 - - - +
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Residues in contact with SER 113 (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* 3.9 7.2 - - - +
44C MET 2.8 14.6 + - - -
45C GLY* 3.3 20.4 - - - -
46C LEU 4.0 1.0 + - - -
83C TYR* 2.8 30.2 + - - -
108C HIS* 5.2 1.0 + - - -
111C ARG* 3.4 6.9 - - - +
112C SER* 1.3 80.7 - - - +
114C PHE* 1.3 64.6 + - - +
115C VAL* 5.5 1.3 - - - -
151C LEU* 4.3 6.7 - - - +
154C LYS* 4.6 4.0 - - - +
155C PRO* 3.5 27.1 - - - -
157C LEU* 5.8 2.2 - - - -
273C LEU* 5.6 0.9 - - - -
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Residues in contact with PHE 114 (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* 3.9 17.7 - - + -
48C ILE* 3.8 21.3 - - + -
100C MET* 5.0 2.7 - - - -
103C VAL* 3.6 23.3 - - + -
108C HIS* 4.3 11.9 - + - +
113C SER* 1.3 78.0 - - - +
115C VAL* 1.3 75.8 + - - +
116C CYS* 3.9 22.4 - - + -
143C PHE* 3.5 38.6 - + - -
151C LEU* 3.7 22.9 - - + -
155C PRO 3.1 8.3 + - - +
156C LYS* 3.5 7.9 - - + -
157C LEU* 2.8 27.8 + - - +
158C PHE* 4.0 14.1 - + - -
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Residues in contact with VAL 115 (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 2.9 12.3 + - - +
47C CYS* 3.3 23.3 - - + -
48C ILE 2.9 23.8 + - - -
78C PHE* 4.1 11.4 - - + -
83C TYR* 3.7 29.8 - - + +
113C SER* 4.9 0.2 - - - +
114C PHE* 1.3 87.1 - - - +
116C CYS* 1.3 64.7 + - - +
117C VAL* 4.1 5.4 - - + -
157C LEU* 3.3 26.0 - - + +
159C ILE* 4.0 26.0 - - + -
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Residues in contact with CYS 116 (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* 3.4 10.5 - - + +
50C ILE* 4.6 2.5 - - - -
100C MET* 4.1 25.8 - - - -
114C PHE* 3.9 12.3 - - + -
115C VAL* 1.3 74.8 - - - +
117C VAL* 1.3 63.3 + - - +
118C LEU* 3.8 31.0 + - - +
139C ILE* 5.4 0.4 - - - -
157C LEU 2.8 10.0 + - - +
158C PHE* 3.3 29.0 - - + -
159C ILE* 2.8 26.7 + - - +
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Residues in contact with VAL 117 (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* 4.4 5.4 - - - -
48C ILE 2.7 15.5 + - - +
49C ILE* 4.3 17.7 - - + +
50C ILE* 2.8 30.5 + - - +
74C LEU* 3.6 33.7 - - + -
78C PHE* 4.6 0.7 - - + -
115C VAL* 4.1 14.8 - - + -
116C CYS* 1.3 77.1 - - - +
118C LEU* 1.3 65.2 + - - +
119C LEU* 3.8 15.9 - - + -
159C ILE* 3.3 34.5 - - + +
216C ILE* 4.6 0.2 - - + -
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Residues in contact with LEU 118 (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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50C ILE* 3.6 36.6 - - + -
96C ILE* 5.1 2.7 - - + -
116C CYS* 3.8 20.0 - - - +
117C VAL* 1.3 72.2 - - - +
119C LEU* 1.3 64.3 + - - +
120C SER 4.0 0.4 - - - -
127C ILE* 4.1 22.0 - - + -
136C LEU* 3.7 30.1 - - + -
139C ILE* 4.6 22.9 - - + -
140C THR* 6.4 0.2 - - + -
158C PHE* 5.0 6.7 - - + -
159C ILE 2.8 11.9 + - - +
160C ILE* 4.2 16.2 - - + -
161C GLN 2.9 30.5 + - - +
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Residues in contact with LEU 119 (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* 4.1 9.0 - - + -
50C ILE* 2.9 16.5 + - - +
51C ASN* 3.7 18.2 - - - +
52C ASN* 2.9 29.3 + - - +
64C ARG* 3.5 8.0 + - - +
67C THR* 3.7 16.4 - - - +
70C ASP* 4.0 5.6 - - + +
71C ALA* 3.9 30.3 - - + +
74C LEU* 4.0 12.3 - - + -
117C VAL* 3.8 21.1 - - + -
118C LEU* 1.3 78.3 - - - +
120C SER* 1.3 64.6 + - - +
161C GLN* 3.6 22.4 - - + -
216C ILE* 4.0 8.3 - - + -
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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