Contacts of the strand formed by residues 118 - 124 (chain A) in PDB entry 1D7E
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 TYR 118 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A ILE 3.8 0.2 - - - +
32A GLN* 3.4 3.0 - - - +
33A LEU* 2.8 47.3 + - - +
34A ASP 3.8 8.3 - - - -
35A GLY* 3.7 24.2 - - - -
79A PHE* 3.7 19.3 - + + -
82A GLY 5.1 0.9 - - - -
83A VAL* 3.6 41.5 + - + +
86A GLY* 6.2 1.6 - - - -
88A LEU* 3.8 24.5 - - + -
110A LYS 3.9 2.9 - - - -
111A LYS* 3.8 29.0 - - + -
112A ALA 4.1 0.4 - - - +
116A ASP 3.9 3.6 + - - -
117A SER* 1.3 95.5 + - - +
119A TRP* 1.3 63.5 + - - +
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Residues in contact with TRP 119 (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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12A GLU* 4.4 17.7 + - + +
15A LEU* 3.8 29.8 - - + +
16A ALA* 5.0 2.7 - - - +
23A LEU* 3.9 37.2 - - + -
30A ALA* 4.4 2.2 - - + -
31A ILE 3.3 23.3 - - - -
32A GLN* 3.7 31.2 - - + -
41A GLN* 3.7 18.2 - - - -
88A LEU* 4.8 1.6 - - - +
108A HIS 4.5 0.2 - - - -
109A MET* 3.2 8.1 - - - +
110A LYS 2.8 43.3 + - - +
111A LYS 4.3 2.0 - - - -
112A ALA* 3.4 28.1 - - + +
118A TYR* 1.3 73.9 - - - +
120A VAL* 1.3 62.1 + - - +
121A PHE* 3.3 40.6 - + + -
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Residues in contact with VAL 120 (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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29A GLY 3.9 0.5 - - - +
30A ALA* 3.6 1.6 - - - -
31A ILE* 2.8 58.6 + - + +
33A LEU* 3.9 30.5 - - + -
62A PHE* 5.0 3.6 - - + -
75A PHE* 3.9 26.5 - - + -
79A PHE* 5.0 2.5 - - + -
107A VAL* 4.1 12.1 - - + -
108A HIS 3.7 2.7 - - - -
109A MET* 3.9 18.6 - - + -
118A TYR 4.9 0.7 - - - +
119A TRP* 1.3 76.8 - - - +
121A PHE* 1.3 61.7 + - - +
122A VAL* 4.3 12.7 + - + +
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Residues in contact with PHE 121 (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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6A PHE* 3.7 20.8 - - + -
11A ILE* 3.7 31.6 - - + -
15A LEU* 3.3 33.7 - - + -
28A PHE* 3.5 18.8 - + + -
29A GLY 3.2 4.5 - - - +
30A ALA* 3.9 10.5 - - + -
107A VAL* 3.3 7.3 - - - +
108A HIS* 2.8 61.9 + - + +
110A LYS* 4.4 7.6 - - + -
119A TRP* 3.3 44.4 - + + -
120A VAL* 1.3 72.2 - - - +
122A VAL* 1.3 64.5 + - - +
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Residues in contact with VAL 122 (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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6A PHE* 3.9 4.0 - - - -
28A PHE* 3.4 2.4 - - - +
29A GLY 2.8 33.3 + - - -
31A ILE* 4.9 1.1 - - + -
46A GLU* 3.3 33.9 - - - +
49A ILE* 4.0 12.1 - - + +
96A PHE* 3.8 24.9 - - + -
105A VAL* 3.7 30.3 - - + -
106A LYS 3.4 4.3 - - - -
107A VAL* 4.7 2.9 - - + -
120A VAL* 4.3 17.5 - - + +
121A PHE* 1.3 81.4 - - - +
123A LYS* 1.3 67.1 + - - +
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Residues in contact with LYS 123 (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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6A PHE* 3.8 43.0 + - + +
27A ALA 5.5 2.0 - - - +
28A PHE* 4.3 9.0 - - + +
49A ILE* 4.6 3.8 - - - -
105A VAL* 3.2 9.3 - - - -
106A LYS* 2.9 62.6 + - + +
122A VAL* 1.3 78.9 - - - +
124A ARG* 1.3 69.7 + - - +
125A VAL* 4.9 0.7 - - - -
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Residues in contact with ARG 124 (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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48A ASP* 3.4 25.5 + - - +
49A ILE* 3.6 34.1 + - + +
103A THR* 3.9 28.8 + - + +
104A LYS 3.8 7.2 - - - +
105A VAL* 4.4 0.9 - - - +
123A LYS* 1.3 86.7 - - - +
125A VAL* 1.3 66.4 + - - +
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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