Contacts of the strand formed by residues 121 - 130 (chain A) in PDB entry 2HZA
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 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A TYR* 3.7 33.0 - - + -
59A VAL 3.5 5.4 - - - +
60A TYR* 3.9 7.4 - - + -
67A LEU* 3.8 25.6 - - + -
71A ILE* 4.0 14.8 - - + -
115A VAL* 4.0 21.8 - - + +
116A ILE* 3.8 21.5 - - + +
118A GLN* 3.7 17.0 - - + +
119A ARG 3.1 1.4 - - - -
120A GLY* 1.3 77.5 + - - +
122A ARG* 1.3 61.4 + - - +
124A GLY 5.4 0.4 + - - +
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Residues in contact with ARG 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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58A TYR* 3.9 1.0 - - - +
59A VAL* 2.8 47.9 + - + +
61A GLU* 4.8 7.7 - - - +
94A ASP* 2.8 41.6 + - - +
120A GLY* 3.7 17.5 + - - +
121A VAL* 1.3 74.8 - - - +
123A HIS* 1.3 92.2 + - + +
124A GLY 3.1 7.1 + - - -
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Residues in contact with HIS 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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57A SER 3.8 2.9 - - - +
58A TYR* 4.2 1.7 - - - -
59A VAL* 3.8 21.1 - - + -
122A ARG* 1.3 109.1 + - + +
124A GLY* 1.3 67.6 + - - +
125A HIS* 3.6 0.3 + - - +
127B GLN* 3.0 20.1 + - - +
129B LEU* 3.7 32.9 - - + +
130B PRO* 5.7 5.1 + - + -
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Residues in contact with GLY 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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57A SER 3.3 9.6 - - - -
58A TYR* 3.9 10.3 - - - -
116A ILE* 3.9 31.4 - - - +
121A VAL* 5.4 0.2 - - - -
122A ARG 3.1 5.3 - - - -
123A HIS* 1.3 79.3 - - - +
125A HIS* 1.3 62.4 + - - +
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Residues in contact with HIS 125 (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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42A GLN* 4.2 14.3 + - - -
55A VAL 3.5 2.3 + - - +
56A LEU* 3.5 7.1 - - - +
57A SER* 2.9 34.8 + - - +
116A ILE* 3.8 6.1 - - - +
124A GLY* 1.3 75.5 - - - +
126A LEU* 1.3 80.1 + - - +
127A GLN* 4.1 11.1 + - + +
125B HIS* 3.6 36.1 + + - -
127B GLN* 2.9 33.3 + - + +
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Residues in contact with LEU 126 (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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42A GLN* 3.3 14.2 + - - -
46A GLN* 4.2 12.9 - - - +
54A ALA* 4.0 22.7 - - + -
55A VAL 3.6 11.0 - - - +
56A LEU* 4.3 8.1 - - + -
108A VAL* 4.4 4.3 - - + -
109A GLN* 3.7 30.5 - - + +
112A ALA* 3.6 33.7 - - + -
113A ASP* 5.9 1.3 - - - +
116A ILE* 4.5 5.2 - - + +
125A HIS* 1.3 91.9 + - - +
127A GLN* 1.3 69.0 + - - +
128A CYS* 3.8 16.8 - - - +
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Residues in contact with GLN 127 (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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42A GLN* 4.8 5.2 - - - +
54A ALA* 3.2 4.3 - - - -
55A VAL* 2.9 44.8 + - + +
125A HIS* 4.1 11.4 - - + +
126A LEU* 1.3 77.6 - - - +
128A CYS* 1.3 60.7 + - - +
129A LEU* 4.1 19.7 - - + +
57B SER* 2.7 29.3 + - - -
123B HIS* 3.0 35.9 + - - +
125B HIS* 3.6 18.6 + - - +
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Residues in contact with CYS 128 (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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45A THR* 3.1 43.3 + - + +
46A GLN* 3.8 21.9 + - - +
53A PHE 3.8 3.1 - - - -
54A ALA* 4.0 4.5 - - - -
105A MSE 3.7 28.5 - - - -
108A VAL* 4.5 2.7 - - - -
126A LEU* 3.8 25.3 - - - -
127A GLN* 1.3 75.2 - - - +
129A LEU* 1.3 66.4 + - - +
130A PRO* 3.2 10.0 - - - +
123B HIS* 6.0 0.2 - - - -
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Residues in contact with LEU 129 (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 GLY* 3.5 0.9 - - - -
53A PHE* 2.6 43.6 + - + +
55A VAL* 4.6 10.8 - - + -
105A MSE 4.0 0.7 - - - -
127A GLN* 4.1 21.1 - - + +
128A CYS* 1.3 80.0 - - - +
130A PRO* 1.3 68.3 - - - +
131A LYS* 4.6 0.5 - - - -
59B VAL* 4.0 11.9 - - + -
96B LEU* 3.8 36.3 - - + -
123B HIS* 3.6 44.4 - - + +
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Residues in contact with PRO 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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44A ALA 5.2 1.3 - - - +
45A THR* 3.3 39.3 - - - +
50A THR* 4.2 16.4 - - + -
51A GLN 3.7 7.0 - - - +
105A MSE 3.9 8.5 - - + -
128A CYS 3.2 11.9 - - - +
129A LEU* 1.3 88.3 - - - +
131A LYS* 1.3 68.8 + - - +
123B HIS* 5.7 8.5 + - + -
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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