Contacts of the strand formed by residues 132 - 143 (chain A) in PDB entry 4FMF
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 GLY 132 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A THR* 2.6 47.9 + - - +
130A PRO 3.4 2.8 + - - -
131A THR* 1.3 80.6 - - - +
133A ASN* 1.3 68.3 + - - -
134A ARG* 5.2 0.2 - - - +
66B THR* 4.5 0.2 - - - -
77B ASN* 3.3 9.9 - - - -
80B ILE* 3.8 17.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A GLU* 2.8 38.5 + - + -
126A PHE 3.2 6.1 - - - +
127A ALA* 3.7 14.8 - - - +
131A THR 4.8 0.7 - - - +
132A GLY* 1.3 77.2 - - - -
134A ARG* 1.3 64.3 + - - +
135A GLU* 4.3 2.9 - - - +
64B GLN* 3.9 0.5 + - - -
66B THR* 3.4 23.2 + - - -
68B GLN* 3.6 21.9 + - - +
77B ASN* 2.7 32.7 + - - +
125B GLU* 2.9 19.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A SER 5.1 2.3 + - - -
53A PHE* 2.8 62.5 - - + +
54A ALA* 3.4 26.2 - - - +
55A ASN* 3.8 3.2 - - - +
124A CYS 3.9 0.9 - - - +
125A GLU* 3.4 1.1 - - - -
126A PHE* 2.7 49.2 + - + +
128A THR* 5.2 0.7 - - + -
132A GLY 5.2 0.9 - - - +
133A ASN* 1.3 75.4 - - - +
135A GLU* 1.3 67.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LYS* 5.3 3.0 + - - -
123A ILE* 3.5 26.5 - - + +
124A CYS 3.2 9.6 - - - +
125A GLU* 3.7 19.0 - - + +
133A ASN* 4.3 2.1 - - - +
134A ARG* 1.3 83.3 - - - +
136A SER* 1.3 62.4 + - - +
137A GLN* 3.8 17.8 + - + +
68B GLN* 4.7 4.7 + - - +
75B LYS* 3.3 38.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A HIS 4.9 4.9 + - - -
51A CYS* 4.1 10.9 - - - +
67A TRP* 5.5 0.5 - - - -
122A TYR 3.7 0.3 - - - +
123A ILE* 3.4 4.5 - - - +
124A CYS* 2.9 46.3 + - - +
135A GLU* 1.3 74.4 - - - +
137A GLN* 1.3 68.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ASN 5.4 4.7 + - - +
37A ASP* 4.2 12.8 + - - +
121A VAL* 3.7 19.5 - - + +
122A TYR 3.2 7.0 - - - +
123A ILE* 3.9 21.1 - - + +
135A GLU* 3.8 19.3 + - + +
136A SER* 1.3 82.7 - - - +
138A LEU* 1.3 66.1 + - - +
139A ASN* 5.7 2.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ASP* 3.3 24.5 - - + +
39A MET* 4.3 17.5 - - + -
49A LEU* 3.5 31.9 - - + -
50A HIS* 3.8 35.0 - - + +
67A TRP* 4.5 4.9 - - + -
121A VAL* 3.6 0.6 - - - -
122A TYR* 2.8 54.9 + - + +
137A GLN* 1.3 76.5 - - - +
139A ASN* 1.3 70.4 + - - +
140A LEU 3.8 0.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ASN 5.2 9.1 - - - +
37A ASP 2.9 9.5 + - - +
38A SER* 3.8 19.9 - - - +
39A MET* 2.7 33.3 + - - +
120A GLY 3.7 4.5 - - - +
121A VAL* 3.8 24.4 - - - +
137A GLN* 5.6 2.8 + - - +
138A LEU* 1.3 78.0 - - - +
140A LEU* 1.3 61.5 + - - +
141A THR* 3.9 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A MET* 3.5 18.8 - - + +
40A TYR 4.8 0.2 - - - -
41A GLY 4.5 5.4 - - - +
47A VAL* 4.4 15.9 - - + -
49A LEU* 4.5 10.1 - - + -
111A LEU* 4.0 22.0 - - + -
114A LEU* 4.0 13.2 - - + -
118A ASP* 3.8 20.4 - - + +
119A GLU* 3.4 8.0 - - - +
120A GLY 2.8 28.4 + - - +
122A TYR* 3.5 27.4 - - + -
138A LEU 3.8 1.0 + - - -
139A ASN* 1.3 74.0 - - - +
141A THR* 1.3 75.6 + - - +
142A VAL* 4.0 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A SER* 5.6 0.7 - - - -
39A MET 2.9 8.0 + - - -
40A TYR* 3.2 40.4 - - + +
41A GLY 3.1 23.6 + - - -
119A GLU* 3.3 20.4 + - - +
139A ASN* 5.0 7.3 + - - +
140A LEU* 1.3 74.4 + - - +
142A VAL* 1.3 64.5 + - - +
143A MET* 3.9 6.2 + - + +
178A LYS* 4.0 9.2 - - - +
179A PRO* 6.3 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A GLY 3.4 8.1 - - - +
43A ILE* 3.1 39.9 - - + +
114A LEU* 4.0 20.2 - - + -
115A GLU 3.6 20.9 - - - +
116A LEU* 3.8 6.5 - - + -
118A ASP* 4.1 4.5 - - + -
119A GLU* 3.0 39.5 + - + +
140A LEU* 4.2 8.1 - - + -
141A THR* 1.3 75.4 - - - +
143A MET* 1.3 60.9 + - - +
178A LYS* 3.3 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A TYR* 3.9 20.6 - - + -
41A GLY* 2.7 42.5 + - - +
42A PHE* 3.4 37.8 - - + +
43A ILE* 2.9 30.5 + - - +
141A THR* 4.6 14.1 - - + +
142A VAL* 1.3 77.2 - - - +
144A ALA* 1.3 61.4 + - - +
178A LYS* 3.4 13.7 - - + +
179A PRO* 4.3 12.1 - - + -
230A TYR* 3.8 3.8 - - - +
231A HIS* 5.2 13.0 - - + +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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