Contacts of the strand formed by residues 98 - 106 (chain A) in PDB entry 2F24
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 LEU 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A LEU* 4.2 5.8 - - + -
28A LEU* 3.4 28.0 - - + -
35A LEU* 3.6 31.6 - - + -
90A LEU 3.4 3.4 - - - +
91A TYR* 3.5 29.6 - - + -
96A GLY 3.8 5.4 - - - +
97A THR* 1.3 75.2 - - - +
99A PHE* 1.3 62.1 + - - +
128A THR* 3.1 10.0 - - - -
129A SER* 3.0 37.6 + - - +
132A HIS* 3.6 10.1 - - + -
133A GLY* 3.6 22.9 - - - +
136A TRP* 4.0 12.9 - - + -
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Residues in contact with PHE 99 (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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26A LEU* 5.1 0.2 - - - +
89A PRO* 3.2 5.4 - - - +
90A LEU* 2.8 43.0 + - + +
92A ASP* 4.1 22.9 - - + -
95A THR* 5.4 0.2 - - - -
97A THR* 4.2 17.9 - - + -
98A LEU* 1.3 79.2 - - - +
100A LEU* 1.3 60.7 + - - +
101A PHE* 3.7 28.7 - + + -
126A GLN* 3.7 23.8 - - + -
127A VAL 3.8 2.2 - - - -
128A THR* 3.5 21.8 - - + -
136A TRP* 4.5 2.3 - - - -
140A ARG* 5.9 0.7 - - - -
174A LEU* 4.1 17.9 - - + -
202A HIS* 3.2 28.7 - - + -
203A GLY* 4.6 5.4 - - - -
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Residues in contact with LEU 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PHE* 3.9 30.3 - - + -
52A ILE* 4.4 10.8 - - + -
74A VAL* 4.2 15.7 - - + -
77A ALA* 4.2 9.6 - - + -
87A PRO* 4.0 13.0 - - + -
88A CYS 3.7 23.1 - - - +
89A PRO* 4.0 13.2 - - + -
99A PHE* 1.3 74.9 - - - +
101A PHE* 1.3 62.1 + - - +
102A PHE* 3.6 5.2 - - + -
126A GLN* 3.3 4.0 - - - +
127A VAL* 2.9 51.4 + - + -
136A TRP* 3.8 12.3 - - + -
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Residues in contact with PHE 101 (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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87A PRO* 3.7 1.0 - - - +
88A CYS* 2.8 60.2 + - + +
90A LEU* 4.5 9.2 - - + -
99A PHE* 3.7 32.3 - + + -
100A LEU* 1.3 75.4 - - - +
102A PHE* 1.3 63.6 + - - +
124A LEU* 4.9 6.7 - - + -
125A CYS 3.3 5.4 - - - +
126A GLN* 3.4 33.4 - - + -
142A LEU* 3.9 11.7 - - + -
159A VAL* 4.4 8.7 - - + -
164A CYS* 3.8 14.8 - - - -
174A LEU* 4.9 2.0 - - + -
176A VAL* 3.7 20.2 - - + -
206A TRP* 3.7 33.7 - + - -
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Residues in contact with PHE 102 (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 ILE* 3.6 17.5 - - + -
77A ALA* 3.5 46.2 - - + -
78A ARG* 3.6 7.2 - - - -
79A LEU* 4.8 0.4 - - + -
84A SER* 3.7 15.3 - - - -
85A MET 3.5 12.1 - - - +
86A ASN 3.7 5.4 - - - +
100A LEU* 3.6 15.3 - - + -
101A PHE* 1.3 76.1 - - - +
103A ILE* 1.3 77.2 + - - +
104A ALA* 4.5 4.3 - - + -
124A LEU* 3.8 5.0 - - - +
125A CYS* 2.9 64.4 + - + -
126A GLN* 3.8 11.2 - - - -
127A VAL* 4.0 8.5 - - + -
139A PRO* 4.4 7.9 - - + -
159A VAL* 4.4 2.6 - - - +
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Residues in contact with ILE 103 (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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83A ARG 3.5 0.5 - - - +
84A SER* 3.4 4.5 - - - -
85A MET* 2.9 52.7 + - + +
86A ASN* 4.2 5.6 - - + -
102A PHE* 1.3 82.0 - - - +
104A ALA* 1.3 63.9 + - - +
105A ILE* 4.0 9.9 - - + -
122A THR* 3.3 24.5 - - + -
123A ARG 3.4 5.8 - - - +
124A LEU* 4.2 4.0 - - + -
157A PHE* 3.6 33.9 - - + +
158A ALA* 3.7 30.5 - - + -
159A VAL* 3.9 17.3 - - + +
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Residues in contact with ALA 104 (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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79A LEU* 3.7 32.1 - - + +
82A HIS* 3.8 13.6 - - + -
83A ARG 3.3 6.1 - - - +
84A SER* 5.1 0.9 - - - +
102A PHE* 4.5 6.7 - - + -
103A ILE* 1.3 75.5 - - - +
105A ILE* 1.3 63.4 + - - +
122A THR* 3.7 1.0 - - - -
123A ARG* 2.8 40.4 + - + +
125A CYS* 4.0 11.7 - - - -
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Residues in contact with ILE 105 (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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82A HIS* 3.2 5.1 - - - -
83A ARG* 2.7 50.3 + - + +
85A MET* 3.8 26.0 - - + -
103A ILE* 4.0 8.7 - - + -
104A ALA* 1.3 79.1 - - - +
106A PRO* 1.3 84.0 - - + +
113A GLN* 5.9 1.1 - - - +
121A VAL* 4.4 10.5 - - + -
122A THR* 3.7 26.5 - - + +
156A THR* 4.3 6.7 - - - +
157A PHE 5.6 0.7 - - - +
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Residues in contact with PRO 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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81A GLY 3.5 9.6 - - - +
82A HIS* 3.4 19.0 - - + +
83A ARG* 3.9 5.9 + - - -
105A ILE* 1.3 103.7 - - + +
107A GLY* 1.3 64.1 + - - +
108A GLN* 3.2 19.3 + - - +
110A THR* 3.7 24.5 - - + -
113A GLN* 5.0 0.9 - - - +
121A VAL* 3.3 30.7 - - + +
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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