Contacts of the strand formed by residues 109 - 113 (chain A) in PDB entry 4M92
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 THR 109 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A MET* 3.5 3.5 - - - +
49A PHE* 2.8 36.5 + - - +
104A MET* 4.2 25.3 - - + +
106A SER 4.4 10.7 + - - -
108A PRO* 1.3 78.0 + - - +
110A PHE* 1.3 66.5 + - - +
111A MET* 4.0 15.0 - - + -
124A THR* 4.0 25.6 - - + -
125A PHE 5.7 0.4 - - - +
127A LEU* 5.4 1.8 - - - -
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Residues in contact with PHE 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ILE* 5.2 2.5 - - + -
47A VAL 3.4 3.8 - - - +
48A MET* 3.4 42.8 - - + -
64A ALA* 3.9 30.1 - - + -
68A TYR* 3.5 30.7 - + + -
108A PRO* 4.9 5.4 - - + -
109A THR* 1.3 78.0 - - - +
111A MET* 1.3 64.0 + - - +
124A THR* 3.6 3.5 - - - +
125A PHE* 3.0 51.8 + + + +
127A LEU* 4.8 9.3 - - + +
132A PHE* 4.3 10.1 - - + -
137A LEU* 3.9 30.1 - - + -
140A TRP* 3.8 11.9 - + + -
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Residues in contact with MET 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A MET 3.8 0.5 - - - +
46A ILE* 3.4 5.4 - - - +
47A VAL* 2.9 33.3 + - - +
49A PHE* 3.7 24.2 - - + -
102A LEU* 4.6 9.9 - - + -
104A MET* 3.8 15.5 - - - -
109A THR* 4.0 9.0 - - + -
110A PHE* 1.3 78.6 - - - +
112A HIS* 1.3 59.2 + - - +
113A PHE* 3.8 30.6 + - + -
119A PRO* 3.9 24.5 - - + -
123A ASP 3.2 5.4 - - - +
124A THR* 3.9 21.8 - - - +
140A TRP* 3.6 5.4 - - - -
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Residues in contact with HIS 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A SER* 2.7 39.6 + - - -
45A MET 3.5 7.6 - - - -
46A ILE* 3.7 20.6 - - + -
111A MET* 1.3 72.4 - - - +
113A PHE* 1.3 64.0 + - - +
114A PRO* 3.5 30.3 - - + +
115A PRO* 5.2 0.2 - - + -
119A PRO* 3.6 7.6 - - - +
123A ASP* 2.8 55.4 + - - +
140A TRP* 3.7 11.6 - - + -
144A ARG* 3.8 28.6 - - + +
145A THR* 3.5 6.2 - - + +
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Residues in contact with PHE 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A PHE* 3.9 15.7 - + - -
36A ILE* 3.5 27.8 - - + +
37A LYS* 3.9 26.5 - - + -
41A ARG* 5.2 4.0 + - - +
43A TYR 4.4 0.9 - - - +
44A SER* 3.6 1.0 - - - -
45A MET* 2.7 34.0 + - + +
47A VAL* 3.7 31.9 - - + -
49A PHE* 4.1 9.0 - + - -
102A LEU* 4.5 6.5 - - + -
111A MET* 3.8 37.9 - - + -
112A HIS* 1.3 76.3 - - - +
114A PRO* 1.3 72.4 - - + +
119A PRO* 3.6 24.7 - - + -
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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