Contacts of the strand formed by residues 129 - 137 (chain A) in PDB entry 2EFP
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 VAL 129 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A VAL* 4.1 7.9 - - + -
70A LYS 3.9 2.7 - - - -
72A LYS* 3.7 13.5 + - - -
81A LEU* 3.5 27.1 - - + -
123A VAL* 3.6 31.4 - - + +
124A MET* 5.3 4.0 - - - +
126A ILE* 3.3 17.3 - - + +
127A PRO 3.0 4.5 + - - +
128A GLU* 1.3 75.5 - - - +
130A GLU* 1.3 65.6 + - - +
131A ARG* 3.7 13.9 - - - +
132A THR* 3.8 23.6 - - + -
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Residues in contact with GLU 130 (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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70A LYS* 2.7 26.4 + - + +
71A ALA 3.9 15.9 - - - +
72A LYS* 2.8 37.8 + - + +
128A GLU 3.6 2.2 + - - -
129A VAL* 1.3 75.1 - - - +
131A ARG* 1.3 73.7 + - + +
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Residues in contact with ARG 131 (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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68A SER 4.0 0.2 - - - +
69A VAL* 3.5 0.5 - - - +
70A LYS* 2.8 52.0 + - + +
129A VAL* 3.6 3.0 - - - -
130A GLU* 1.3 91.4 - - + +
132A THR* 1.3 94.3 + - - +
133A SER* 5.7 0.9 - - - -
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Residues in contact with THR 132 (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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67A THR* 4.0 11.9 - - + -
68A SER 3.2 8.3 - - - -
69A VAL* 4.1 11.9 - - + -
119A PHE* 6.1 0.4 - - + -
120A LEU* 4.5 16.6 - - - +
123A VAL* 3.6 31.6 - - + -
124A MET* 5.1 7.0 - - + +
129A VAL* 3.8 11.0 - - + -
131A ARG* 1.3 107.6 + - - +
133A SER* 1.3 61.9 + - - +
134A THR* 4.2 1.3 + - - -
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Residues in contact with SER 133 (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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66A ILE 3.9 1.6 - - - +
67A THR* 3.5 1.1 - - - -
68A SER* 2.8 45.3 + - - -
70A LYS* 6.5 1.3 - - - -
101A ASN* 5.7 1.3 - - - -
131A ARG* 5.7 0.9 - - - -
132A THR* 1.3 76.2 - - - +
134A THR* 1.3 63.8 + - - +
135A GLN* 4.0 6.4 + - - +
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Residues in contact with THR 134 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A VAL* 3.6 31.4 - - + -
66A ILE 3.7 0.4 - - - -
67A THR* 2.8 32.0 + - - +
115A PHE* 4.0 19.3 - - + -
120A LEU* 4.5 9.5 - - - +
132A THR* 4.2 1.4 + - - -
133A SER* 1.3 74.2 + - - +
135A GLN* 1.3 67.5 + - - +
136A VAL* 4.0 9.4 + - + +
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Residues in contact with GLN 135 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A VAL* 3.6 1.4 - - - -
66A ILE* 2.9 57.2 + - + +
68A SER* 4.6 11.9 + - - -
133A SER* 5.0 7.4 - - - +
134A THR* 1.3 76.3 - - - +
136A VAL* 1.3 65.4 + - - +
137A VAL* 3.6 1.7 + - + +
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Residues in contact with VAL 136 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A TYR* 4.3 30.3 - - + +
64A ILE 3.7 10.1 - - - +
65A VAL* 4.5 13.0 - - + -
115A PHE* 6.4 0.4 - - + -
134A THR* 4.0 8.9 + - + +
135A GLN* 1.3 73.8 - - - +
137A VAL* 1.3 74.4 + - - +
138A VAL* 3.4 18.7 + - + +
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Residues in contact with VAL 137 (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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62A ASP 5.1 3.5 - - - +
64A ILE* 2.8 45.3 + - + +
66A ILE* 3.7 36.6 - - + -
135A GLN 4.4 1.1 - - - +
136A VAL* 1.3 77.9 - - - +
138A VAL* 1.3 61.1 + - - +
139A LYS 3.7 27.4 - - - +
140A ILE* 4.0 17.3 - - + -
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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