Contacts of the strand formed by residues 48 - 57 (chain A) in PDB entry 2HW6
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 48 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A PHE* 2.9 49.2 + + + +
45A GLU* 4.0 6.6 - - - +
47A MET* 1.3 95.7 - - + +
49A LYS* 1.3 60.1 + - - +
50A LEU 4.0 0.2 - - - -
66A ALA* 4.1 17.9 - - + -
67A VAL 3.3 6.1 - - - +
68A SER* 3.7 26.7 + - - -
69A LEU* 4.0 5.4 - - - -
75A TYR* 3.9 26.9 - + - -
111A ILE* 5.3 2.4 - - - +
112A GLU* 2.6 33.2 + - - +
114A PHE* 6.3 0.4 - - + -
123A VAL* 3.8 28.8 - - + +
83B GLN* 3.6 16.8 + - - +
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Residues in contact with LYS 49 (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 GLU* 4.5 13.6 + - - +
48A TYR* 1.3 72.3 - - - +
50A LEU* 1.3 72.4 + - - +
51A THR* 3.5 2.3 + - + +
66A ALA* 3.2 2.4 - - - -
67A VAL* 2.7 46.6 + - + +
69A LEU* 3.8 24.1 - - + +
83B GLN* 3.3 44.3 + - - +
222B MET 5.8 0.2 - - - +
223B ALA* 4.6 17.3 - - + -
224B PRO* 6.0 0.4 - - + -
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Residues in contact with LEU 50 (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 PHE* 3.9 19.3 - - + -
49A LYS* 1.3 79.9 - - - +
51A THR* 1.3 60.7 + - - +
64A GLN* 3.8 31.0 - - + +
65A GLY 3.3 5.4 - - - +
66A ALA* 3.8 20.4 - - + -
77A VAL* 3.9 12.6 - - + -
79A ILE* 4.0 19.1 - - + -
119A ARG* 5.6 1.8 - - - +
59B ALA 5.2 1.6 - - - +
81B GLU* 4.1 21.8 - - + +
83B GLN* 3.0 34.7 + - + +
223B ALA* 4.3 1.0 - - - +
224B PRO* 3.1 22.0 - - + +
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Residues in contact with THR 51 (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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49A LYS* 4.0 1.8 - - + +
50A LEU* 1.3 74.0 - - - +
52A SER* 1.3 58.3 + - - +
53A GLU* 3.0 26.0 + - - +
64A GLN* 2.9 26.2 + - - +
65A GLY* 2.6 30.1 + - - +
66A ALA 4.1 0.2 - - - +
67A VAL* 3.6 30.3 - - + -
74A GLU* 3.9 14.1 + - - +
221B TYR* 4.4 12.1 - - - +
222B MET 4.4 16.6 - - - +
224B PRO* 3.7 4.8 - - - +
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Residues in contact with SER 52 (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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51A THR* 1.3 74.3 - - - +
53A GLU* 1.3 57.2 + - - +
54A LEU 3.2 7.3 + - - -
59B ALA* 3.7 22.4 - - - +
196B SER* 4.2 19.9 + - - -
221B TYR* 3.5 32.0 - - - +
222B MET* 3.9 8.2 + - - +
223B ALA* 3.4 27.2 + - - +
224B PRO* 3.7 5.5 - - - +
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Residues in contact with GLU 53 (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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51A THR* 3.0 12.8 - - - +
52A SER* 1.3 75.5 - - - +
54A LEU* 1.3 63.0 + - - +
55A LEU* 3.7 23.5 + - + +
64A GLN* 3.5 4.0 - - - +
65A GLY* 2.8 32.9 + - - -
74A GLU* 4.2 5.9 - - - +
126A LYS* 3.0 38.6 + - - -
221B TYR* 3.6 36.8 + - + +
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Residues in contact with LEU 54 (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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52A SER 3.2 9.0 + - - +
53A GLU* 1.3 74.1 - - - +
55A LEU* 1.3 60.4 + - - +
56A GLY* 3.7 17.7 + - - +
57A GLU* 4.0 5.8 - - + +
62A LYS* 4.0 23.8 - - + -
63A VAL 3.4 16.8 - - - +
64A GLN* 4.1 11.9 - - + +
57B GLU* 3.8 30.1 - - + +
58B GLY* 3.9 24.7 - - - +
59B ALA* 4.8 8.5 - - - +
196B SER* 4.6 13.9 + - - +
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Residues in contact with LEU 55 (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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53A GLU* 3.7 26.7 + - - +
54A LEU* 1.3 73.2 - - - +
56A GLY* 1.3 55.1 + - - +
63A VAL* 2.8 38.7 + - + +
64A GLN 4.0 19.5 - - - -
65A GLY* 4.0 6.5 - - - +
76A ALA* 4.2 13.5 - - + -
126A LYS* 5.0 8.3 - - + +
127A LEU 5.8 2.9 - - - +
130A GLY* 6.2 4.7 - - - -
192A PHE* 5.8 5.2 - - + -
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Residues in contact with GLY 56 (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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54A LEU* 3.4 8.5 + - - +
55A LEU* 1.3 81.1 - - - +
57A GLU* 1.3 60.4 + - - -
62A LYS* 3.2 4.7 - - - +
63A VAL 2.8 27.8 + - - +
194A LEU* 3.7 16.4 - - - -
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Residues in contact with GLU 57 (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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54A LEU* 4.0 5.1 - - + +
56A GLY* 1.3 75.9 - - - +
58A GLY* 1.3 71.2 + - - +
61A ALA 3.5 4.7 - - - +
62A LYS* 3.3 33.7 + - + +
194A LEU* 3.9 5.7 - - - +
54B LEU* 3.7 14.9 - - + +
57B GLU* 2.8 56.8 + - + +
58B GLY 3.8 12.3 + - - +
61B ALA 5.0 0.2 - - - -
62B LYS* 3.4 32.0 + - - +
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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