Contacts of the strand formed by residues 100 - 107 (chain E) in PDB entry 4QRR
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 ALA 100 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43E GLN* 3.8 20.2 - - + +
44E GLN 3.4 3.4 - - - +
45E THR* 2.9 36.3 - - + +
46E PRO* 6.3 0.7 - - - -
98E ASP 2.9 11.0 + - - +
99E SER* 1.3 69.4 - - - +
101E LEU* 1.4 61.4 + - - +
102E TYR* 3.7 8.3 - - + -
123E ARG* 3.9 12.1 - - - +
124E LEU* 3.0 30.0 + - - +
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Residues in contact with LEU 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D LYS* 3.8 33.9 - - + +
44E GLN* 2.8 54.8 + - + +
100E ALA* 1.4 69.9 - - - +
102E TYR* 1.3 58.7 + - - +
103E LEU* 3.3 38.5 + - + -
120E PRO 5.0 1.8 - - - +
121E GLY* 4.5 5.4 - - - -
122E THR 3.9 10.3 - - - +
123E ARG* 3.6 52.6 - - + +
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Residues in contact with TYR 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E GLN* 2.7 31.0 + - - -
21E LEU* 3.7 26.0 - - + -
41E TRP* 4.6 1.8 - - + -
42E TYR 3.5 3.1 - - - +
43E GLN* 3.1 33.7 + - + -
53E LEU* 4.0 9.9 - - + -
76E PHE* 3.4 30.5 - + - -
89E MET* 3.9 24.0 - - + -
91E VAL* 4.7 5.6 - - + +
98E ASP* 2.8 36.0 + - - +
100E ALA* 3.7 14.8 - - + -
101E LEU* 1.3 67.7 - - - +
103E LEU* 1.3 56.0 + - - +
122E THR* 3.1 23.0 + - - +
124E LEU* 3.7 22.1 - - + +
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Residues in contact with LEU 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D GLN* 4.3 2.7 - - - +
48D LYS 4.5 10.8 - - - +
50D MET* 4.8 6.1 - - + -
6E GLN* 4.2 2.0 - - - +
41E TRP* 3.6 5.6 - - - -
42E TYR* 2.8 43.8 + - + +
44E GLN* 3.4 43.1 - - + +
50E LEU* 3.9 17.3 - - + -
101E LEU* 3.3 20.5 + - + -
102E TYR* 1.3 73.2 - - - +
104E CYS* 1.3 58.3 + - - +
118E PHE* 4.1 23.8 - - + -
119E GLY 4.0 20.2 - - - +
121E GLY* 4.4 6.7 - - - -
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Residues in contact with CYS 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E VAL* 4.6 1.0 - - - +
6E GLN* 3.3 19.4 + - - +
23E CYS* 3.1 32.3 - - - -
39E VAL* 3.6 12.1 - - - -
40E SER 3.3 16.2 - - - -
41E TRP* 3.5 35.9 - - + -
42E TYR 4.9 0.2 - - - +
103E LEU* 1.3 75.9 - - - +
105E ALA* 1.3 60.7 + - - +
118E PHE* 3.4 5.5 - - - -
119E GLY* 2.9 27.0 + - - -
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Residues in contact with ALA 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E VAL* 5.4 1.8 - - - -
39E VAL* 3.5 6.0 - - - +
40E SER* 2.8 43.4 + - - +
42E TYR* 4.4 5.2 - - + -
104E CYS* 1.3 76.7 - - - +
106E SER* 1.3 60.0 + - - +
107E SER 4.3 0.3 + - - -
116E GLN* 3.7 28.0 - - + -
117E PHE 3.3 8.1 - - - +
118E PHE* 3.7 25.8 - - + -
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Residues in contact with SER 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E VAL* 3.7 24.0 - - - +
25E PRO* 3.3 23.6 - - - +
26E ILE* 3.4 3.0 + - - -
29E HIS* 2.8 38.3 + - - +
31E SER 3.5 4.5 - - - -
39E VAL* 5.7 0.4 - - - -
105E ALA* 1.3 73.6 - - - +
107E SER* 1.3 59.3 + - - +
116E GLN* 3.7 3.3 - - - -
117E PHE* 2.8 31.3 + - - +
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Residues in contact with SER 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E HIS* 3.4 12.8 - - - +
31E SER* 2.9 50.2 + - - +
40E SER* 5.3 1.3 - - - -
105E ALA 4.3 0.2 - - - -
106E SER* 1.3 74.7 + - - +
108E LEU* 1.3 61.7 + - - +
109E GLU 3.5 0.2 - - - -
110E GLY* 3.3 13.0 + - - -
114E ASN* 3.2 25.3 - - - +
115E GLU 4.2 4.4 + - - -
116E GLN* 4.1 20.6 + - - -
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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