Contacts of the strand formed by residues 105 - 113 (chain A) in PDB entry 4QAE
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 SER 105 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A LEU* 4.7 5.4 - - - -
97A ILE* 4.0 16.8 - - - -
98A LYS 4.0 20.6 - - - -
99A SER* 4.2 13.7 + - - -
103A ARG 3.6 5.8 + - - -
104A THR* 1.3 79.1 - - - +
106A GLY* 1.3 60.5 + - - +
125A VAL* 3.2 8.2 - - - +
126A VAL* 3.0 44.5 + - - +
8P ILE* 5.0 4.8 - - - +
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Residues in contact with GLY 106 (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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93A THR* 3.3 13.0 - - - +
94A LEU* 3.3 46.7 + - - +
97A ILE 4.5 2.6 + - - +
105A SER* 1.3 79.0 - - - +
107A LEU* 1.3 60.9 + - - +
124A LYS 3.2 11.2 - - - -
125A VAL* 4.2 0.7 - - - -
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Residues in contact with LEU 107 (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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13A LEU* 3.8 36.3 - - + -
91A GLU* 3.7 23.6 - - + +
92A PHE 3.5 14.8 - - - +
93A THR* 4.2 12.3 - - + -
94A LEU* 4.6 0.4 - - - +
98A LYS* 6.1 1.6 - - - +
106A GLY* 1.3 73.2 - - - +
108A VAL* 1.3 72.0 + - - +
109A ARG* 4.1 15.9 - - + +
122A PHE* 4.4 5.6 - - + -
123A PHE* 3.4 5.9 - - - +
124A LYS* 2.8 50.3 + - + +
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Residues in contact with VAL 108 (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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56A TYR* 4.9 2.5 - - + +
83A PHE* 3.9 38.4 - - + -
91A GLU* 3.1 7.6 - - - +
92A PHE* 2.8 49.1 + - + +
94A LEU* 4.1 12.6 - - + -
107A LEU* 1.3 79.4 - - - +
109A ARG* 1.3 69.5 + - - +
110A VAL* 5.0 2.9 - - + +
121A VAL* 3.7 23.1 - - + -
122A PHE 3.3 4.0 - - - -
123A PHE* 3.8 20.9 - - + -
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Residues in contact with ARG 109 (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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13A LEU* 3.2 44.1 + - - +
16A VAL* 2.8 54.3 + - + -
17A PRO 4.6 1.8 - - - +
18A LEU* 3.5 29.7 - - + +
87A SER* 4.8 2.4 + - - -
88A GLN* 3.4 15.8 + - - -
90A GLY 3.5 3.8 - - - -
91A GLU* 2.7 29.4 + - + +
107A LEU* 4.1 14.1 - - + +
108A VAL* 1.3 79.6 - - - +
110A VAL* 1.3 61.3 + - - +
111A VAL* 3.2 5.7 + - - +
121A VAL* 3.4 3.8 - - - -
122A PHE* 2.8 41.9 + - + +
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Residues in contact with VAL 110 (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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17A PRO 4.3 0.2 - - - -
18A LEU* 3.5 7.2 - - - +
19A GLN* 2.8 27.0 + - + +
22A PHE* 3.9 38.4 - - + -
27A PHE* 4.0 35.9 - - + -
56A TYR* 6.0 0.7 - - + -
90A GLY* 2.9 21.6 + - - +
92A PHE* 4.8 7.0 - - + -
108A VAL* 5.2 3.6 - - + -
109A ARG* 1.3 69.2 - - - +
111A VAL* 1.3 59.0 + - - +
112A SER 4.4 4.0 - - - +
113A THR* 4.1 14.1 - - + -
120A MET 3.9 7.2 - - - +
121A VAL* 4.4 9.4 - - + -
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Residues in contact with VAL 111 (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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16A VAL* 3.7 22.2 - - + -
17A PRO* 3.3 42.3 - - + +
18A LEU 3.8 2.9 - - - +
19A GLN* 3.2 17.2 + - - +
109A ARG 3.2 10.1 + - - +
110A VAL* 1.3 73.2 - - - +
112A SER* 1.3 64.1 + - - +
120A MET* 2.8 27.5 + - + +
122A PHE* 4.0 7.4 - - + +
155A PHE* 3.9 26.2 - - + -
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Residues in contact with SER 112 (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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19A GLN* 3.3 10.2 + - - -
110A VAL* 3.5 2.6 - - - +
111A VAL* 1.3 83.5 - - - +
113A THR* 1.3 67.3 + - - +
118A HIS* 4.3 13.6 - - - -
119A ALA* 3.2 1.3 - - - +
120A MET* 2.8 51.9 + - - +
151A ASN* 5.7 1.4 + - - -
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Residues in contact with THR 113 (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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19A GLN* 2.9 27.7 + - + +
22A PHE* 4.7 0.4 - - + -
27A PHE* 4.0 10.9 - - + -
31A TRP* 3.8 3.3 - - - -
110A VAL* 4.1 10.8 - - + -
112A SER* 1.3 79.7 + - - +
114A ASN* 1.3 57.0 + - - +
115A TYR* 2.9 50.1 + - + -
118A HIS* 2.6 27.4 + - - -
119A ALA* 3.5 12.9 - - - +
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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