Contacts of the strand formed by residues 124 - 128 (chain A) in PDB entry 4UML
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 PHE 124 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A THR* 2.8 23.6 + - + +
70A ALA* 3.2 8.0 - - + -
71A ILE 3.1 21.7 + - - -
114A LEU* 3.5 32.8 - - + -
115A THR 3.3 19.3 - - - +
116A LYS* 4.4 9.6 - - + -
117A GLY* 3.9 3.1 - - - +
122A ALA* 3.8 7.6 - - - +
123A ARG* 1.3 109.1 - - + +
125A ILE* 1.3 64.8 + - - +
159A GLN* 4.0 22.9 - - + -
161A MET* 3.6 23.3 - - + -
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Residues in contact with ILE 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ILE* 3.2 11.7 - - + +
73A ASN* 3.7 20.6 - - + +
89A ILE* 3.9 16.6 - - + -
93A ALA* 4.4 3.1 - - + -
97A LEU* 4.1 19.5 - - + -
113A LYS 3.7 0.9 - - - +
114A LEU* 3.5 4.0 - - - +
115A THR* 2.9 39.6 + - - +
116A LYS 3.8 16.4 + - - +
117A GLY* 4.1 2.2 - - - -
120A LEU* 3.5 34.1 - - + -
124A PHE* 1.3 75.3 - - - +
126A ILE* 1.3 63.8 + - - +
127A HIS* 3.4 26.8 - - + +
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Residues in contact with ILE 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ALA* 3.7 22.2 - - + -
71A ILE 2.7 11.8 + - - +
72A VAL* 3.2 10.6 - - + +
73A ASN 2.9 26.1 + - - +
112A ALA* 3.7 28.7 - - + -
113A LYS 3.5 2.0 - - - -
114A LEU* 3.8 17.7 - - + -
125A ILE* 1.3 74.0 - - - +
127A HIS* 1.3 61.0 + - - +
152A VAL* 3.8 43.1 - - + +
155A LEU* 3.8 13.9 - - + -
156A ALA* 4.6 2.0 - - + +
161A MET* 4.1 14.4 - - + -
164A VAL* 4.9 3.8 - - + -
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Residues in contact with HIS 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ASN* 3.2 31.8 + - + +
79A LEU* 4.2 21.4 - - + +
89A ILE* 5.5 0.2 - - + -
90A PHE* 4.6 6.3 - + - -
97A LEU* 4.6 4.0 - - + -
101A LEU* 3.7 23.4 - - + +
104A LEU* 4.5 2.2 - - + -
107A CYS* 4.0 5.4 - - - -
111A GLU 3.9 0.3 - - - +
112A ALA* 3.2 4.3 - - - -
113A LYS* 2.8 49.7 + - + +
115A THR* 2.8 42.2 + - + +
125A ILE* 3.4 28.6 - - + +
126A ILE* 1.3 72.4 - - - +
128A THR* 1.3 59.2 + - - +
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Residues in contact with THR 128 (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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72A VAL* 4.0 7.6 - - + -
73A ASN 2.9 17.4 + - - +
74A THR* 3.4 2.1 - - - +
75A SER* 2.9 26.2 + - - -
107A CYS* 4.3 2.0 - - - -
111A GLU 2.9 21.4 + - - -
112A ALA* 4.4 7.4 - - - -
127A HIS* 1.3 75.6 - - - +
129A VAL* 1.3 68.7 + - - +
148A CYS* 3.5 20.2 + - + +
152A VAL* 4.5 5.2 - - + -
169A ILE* 3.8 39.7 - - + -
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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