Contacts of the strand formed by residues 21 - 32 (chain A) in PDB entry 4FPR
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 21 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A ALA 4.8 4.5 - - - +
20A TYR* 1.3 81.1 - - - +
22A CYS* 1.3 59.6 + - - +
23A ARG* 4.9 7.5 - - + +
101A GLU* 5.1 2.9 + - - +
102A PHE* 3.5 19.2 - - - -
139A THR* 3.7 36.3 - - + +
140A ARG 3.6 11.9 - - - +
141A GLY* 6.0 0.9 - - - -
142A CYS* 3.6 2.7 - - - -
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Residues in contact with CYS 22 (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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21A VAL* 1.3 73.5 - - - +
23A ARG* 1.3 70.4 + - - +
98A ARG* 3.5 21.3 - - - -
99A TYR 2.9 21.5 - - - +
100A ARG* 3.5 18.2 - - - -
101A GLU 5.2 0.2 - - - +
139A THR* 3.4 4.9 - - - -
140A ARG* 2.8 27.7 + - - -
141A GLY 3.7 11.9 - - - +
142A CYS* 2.0 49.1 - - - -
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Residues in contact with ARG 23 (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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21A VAL* 4.9 7.0 - - + +
22A CYS* 1.3 82.6 - - - +
24A GLU* 1.3 62.0 + - - +
97A HIS 3.5 3.1 - - - +
99A TYR* 3.0 36.0 + - + +
101A GLU* 4.0 28.6 - - + +
133A VAL* 3.8 25.8 - - + +
134A ASN 4.4 6.2 + - - +
135A MET* 3.2 49.3 + - - +
137A ALA 4.5 9.0 + - - +
138A ARG 5.1 0.4 - - - -
139A THR* 3.9 28.9 - - + +
140A ARG* 3.7 12.3 - - - +
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Residues in contact with GLU 24 (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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23A ARG* 1.3 75.0 - - - +
25A ALA* 1.3 66.6 + - - +
26A SER* 5.1 2.1 + - - -
95A THR* 3.7 27.0 - - + +
96A ALA 3.5 5.6 - - - +
97A HIS* 4.4 11.2 + - - +
133A VAL* 3.6 4.2 - - - +
134A ASN* 2.7 53.2 + - + +
137A ALA* 4.2 12.0 - - + +
140A ARG* 4.0 27.0 + - - +
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Residues in contact with ALA 25 (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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23A ARG 3.8 0.4 + - - -
24A GLU* 1.3 79.5 - - - +
26A SER* 1.3 60.3 + - - +
95A THR* 3.3 4.2 - - - +
96A ALA* 2.5 40.7 + - - +
99A TYR* 3.5 43.1 - - + -
131A TRP* 4.1 6.1 - - + -
132A VAL 3.2 14.6 - - - +
133A VAL* 4.0 5.8 - - + -
134A ASN* 4.4 0.4 - - - +
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Residues in contact with SER 26 (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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24A GLU* 5.1 2.8 + - - -
25A ALA* 1.3 72.4 + - - +
27A ILE* 1.3 61.3 + - - +
28A SER* 5.5 0.7 - - - -
93A LYS* 3.6 25.7 - - - -
94A ILE 3.1 6.9 + - - -
95A THR* 2.6 32.6 + - - +
130A GLU 3.4 1.2 - - - +
131A TRP* 3.5 4.3 - - - -
132A VAL* 2.7 45.4 + - - +
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Residues in contact with ILE 27 (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 SER* 1.3 76.4 - - - +
28A SER* 1.3 65.7 + - - +
55A LEU* 3.9 13.5 - - + -
92A CYS 4.0 0.5 - - - +
93A LYS* 3.5 1.5 - - - -
94A ILE* 2.9 36.1 + - + +
111A PHE* 3.7 34.3 - - + -
119A PHE* 4.2 13.0 - - + -
129A PRO* 4.1 11.0 - - + +
130A GLU* 3.5 24.0 - - - +
131A TRP* 3.5 52.7 - - + +
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Residues in contact with SER 28 (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 SER* 5.5 0.3 - - - -
27A ILE* 1.3 77.3 - - - +
29A GLY* 1.3 58.4 + - - +
91A THR* 4.6 6.2 - - - +
92A CYS 3.3 7.2 - - - -
93A LYS* 3.5 27.5 - - - +
119A PHE* 4.0 4.0 - - - -
122A GLU* 3.4 22.8 - - - +
129A PRO* 3.2 24.9 - - - +
130A GLU 4.4 3.1 + - - +
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Residues in contact with GLY 29 (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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28A SER* 1.3 76.5 - - - +
30A GLU* 1.3 60.9 + - - -
91A THR* 3.5 5.0 - - - +
92A CYS* 2.8 32.4 + - - -
119A PHE* 3.3 22.9 - - - -
120A ARG 3.6 10.1 - - - -
122A GLU* 3.9 9.1 + - - -
129A PRO* 4.3 2.2 - - - -
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Residues in contact with GLU 30 (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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29A GLY* 1.3 75.1 - - - -
31A ILE* 1.3 66.8 - - - +
32A ARG* 3.2 31.6 + - - -
89A LEU* 3.4 21.2 - - + +
90A CYS 3.2 11.4 - - - +
91A THR* 4.7 3.5 + - - +
118A ILE 4.2 0.9 - - - +
119A PHE* 3.1 4.7 - - - -
120A ARG* 2.8 44.8 + - - +
121A GLN 3.8 2.0 - - - +
122A GLU* 3.7 15.7 - - + +
123A THR* 2.5 51.2 + - - +
135D MET* 5.4 2.1 - - - +
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Residues in contact with ILE 31 (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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30A GLU* 1.3 80.3 - - - +
32A ARG* 1.3 67.7 + - - +
33A TYR* 3.7 29.9 - - + +
44A ALA 5.4 0.7 - - - +
47A ASP* 4.3 6.3 - - + +
48A CYS* 4.2 24.7 - - + +
51A VAL* 4.3 2.0 - - + -
88A VAL 3.8 0.9 - - - +
89A LEU* 3.7 1.0 - - - -
90A CYS* 2.8 40.4 + - + +
92A CYS* 4.4 8.5 - - + -
118A ILE* 4.0 33.9 - - + +
119A PHE* 3.7 22.7 - - + +
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Residues in contact with ARG 32 (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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30A GLU* 3.2 24.9 + - - +
31A ILE* 1.3 80.1 - - - +
33A TYR* 1.3 69.3 + - - +
34A PRO* 4.6 1.2 - - - +
87A VAL* 4.1 11.7 - - + -
88A VAL 3.5 2.7 - - - -
89A LEU* 3.1 28.5 - - + +
120A ARG* 3.7 46.2 - - - +
121A GLN 3.7 21.2 + - - -
123A THR* 4.5 4.8 + - - -
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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