Contacts of the strand formed by residues 104 - 108 (chain P) in PDB entry 3QUM
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 MET 104 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53P LEU* 3.4 12.7 - - - +
54P THR* 2.9 41.2 + - - +
55P ALA 3.2 24.5 - - - +
56P ALA* 3.7 8.5 - - - +
58P CYS* 3.8 6.3 - - + +
59P ILE* 3.5 42.0 - - + +
88P SER* 3.5 23.3 - - - -
89P PHE 3.4 11.0 - - - +
90P PRO* 4.3 5.4 - - + -
103P LEU* 1.3 76.9 - - - +
105P LEU* 1.3 65.4 + - - +
106P LEU* 3.4 26.1 + - + -
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Residues in contact with LEU 105 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47P VAL* 4.7 3.6 - - + -
51P TRP* 4.0 33.9 - - + -
52P VAL 3.6 15.9 - - - +
53P LEU* 3.8 17.0 - - + -
89P PHE* 2.7 52.3 + - + +
104P MET* 1.3 70.0 - - - +
106P LEU* 1.3 62.4 + - - +
107P ARG 4.3 0.2 - - - -
237P TRP* 3.4 30.5 - - + -
238P ILE* 3.9 22.0 - - + -
241P THR* 3.8 21.1 - - + +
242P ILE* 4.6 6.3 - - + -
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Residues in contact with LEU 106 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33P VAL* 4.1 26.2 - - + -
51P TRP* 3.2 9.2 - - - -
52P VAL* 2.8 50.9 + - + +
54P THR* 4.0 17.5 - - - +
63P SER* 5.7 1.1 - - - +
65P ILE* 4.2 13.9 - - + -
85P VAL* 3.9 18.8 - - + -
87P HIS 3.9 2.5 - - - -
88P SER* 4.0 9.0 - - - -
104P MET* 3.4 33.0 - - + -
105P LEU* 1.3 81.2 - - - +
107P ARG* 1.3 60.4 + - - +
108P LEU* 3.8 4.4 + - + +
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Residues in contact with ARG 107 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B SER* 5.3 3.6 - - - -
31B SER* 5.3 6.9 + - - +
53B SER* 3.4 11.3 + - - -
50P GLN* 3.6 12.6 - - + +
51P TRP* 3.3 38.2 - - + -
85P VAL* 4.0 2.6 - - - +
86P SER* 3.0 42.4 + - - -
87P HIS* 2.9 46.5 + - - +
89P PHE* 4.2 2.2 - - + -
106P LEU* 1.3 69.9 - - - +
108P LEU* 1.3 87.8 + - - +
109P SER 5.2 1.3 - - - -
245P ASN* 2.6 36.1 + - - +
246P PRO* 4.1 16.8 + - - +
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Residues in contact with LEU 108 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46P LEU* 4.6 4.3 - - + -
49P PRO 4.2 5.6 - - - +
50P GLN* 2.7 61.8 + - - +
51P TRP* 3.5 14.6 - - - +
52P VAL* 4.0 11.2 - - + -
65P ILE* 3.4 39.0 - - + -
67P LEU* 5.6 2.2 - - + -
83P PHE* 4.5 16.4 - - + +
84P GLN 4.0 7.6 - - - +
85P VAL* 4.9 4.9 - - + -
86P SER* 4.6 0.2 - - - -
106P LEU* 4.6 4.9 - - + +
107P ARG* 1.3 84.8 - - - +
109P SER* 1.3 67.3 + - - +
110P GLU 3.9 15.0 - - - +
112P ALA* 6.2 1.3 - - + -
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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